HEADER OXIDOREDUCTASE 28-SEP-04 1XKD TITLE TERNARY COMPLEX OF ISOCITRATE DEHYDROGENASE FROM THE HYPERTHERMOPHILE TITLE 2 AEROPYRUM PERNIX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.1.1.42; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 3 ORGANISM_TAXID: 272557; SOURCE 4 STRAIN: K1; SOURCE 5 GENE: BAA79665; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS ENZYME, TERNARY COMPLEX, ISOCITRATE, CA2+, NADP+, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KARLSTROM,R.STOKKE,I.H.STEEN,N.-K.BIRKELAND,R.LADENSTEIN REVDAT 6 23-AUG-23 1XKD 1 REMARK LINK REVDAT 5 07-MAR-18 1XKD 1 REMARK REVDAT 4 13-JUL-11 1XKD 1 VERSN REVDAT 3 24-FEB-09 1XKD 1 VERSN REVDAT 2 01-NOV-05 1XKD 1 JRNL REVDAT 1 04-OCT-05 1XKD 0 JRNL AUTH M.KARLSTROM,R.STOKKE,I.H.STEEN,N.-K.BIRKELAND,R.LADENSTEIN JRNL TITL ISOCITRATE DEHYDROGENASE FROM THE HYPERTHERMOPHILE AEROPYRUM JRNL TITL 2 PERNIX: X-RAY STRUCTURE ANALYSIS OF A TERNARY JRNL TITL 3 ENZYME-SUBSTRATE COMPLEX AND THERMAL STABILITY. JRNL REF J.MOL.BIOL. V. 345 559 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 15581899 JRNL DOI 10.1016/J.JMB.2004.10.025 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 42860 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2289 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3123 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 155 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6568 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 124 REMARK 3 SOLVENT ATOMS : 196 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 45.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.93 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : 0.60000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.348 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.231 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.155 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6733 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9160 ; 1.928 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 840 ; 5.983 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1013 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5111 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3398 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 345 ; 0.150 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 10 ; 0.185 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 43 ; 0.207 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.156 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4189 ; 0.540 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6717 ; 0.977 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2544 ; 1.668 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2443 ; 2.604 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 3 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 141 A 257 2 REMARK 3 1 B 141 B 257 2 REMARK 3 2 A 258 A 278 5 REMARK 3 2 B 258 B 278 5 REMARK 3 3 A 279 A 320 2 REMARK 3 3 B 279 B 320 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 636 ; 0.09 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 734 ; 0.63 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 71 ; 1.18 ; 5.00 REMARK 3 TIGHT THERMAL 1 A (A**2): 636 ; 0.33 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 734 ; 0.97 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 71 ; 2.42 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 13 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 131 REMARK 3 ORIGIN FOR THE GROUP (A): 258.6029 93.4280-137.8816 REMARK 3 T TENSOR REMARK 3 T11: 0.1396 T22: 0.2108 REMARK 3 T33: 0.0967 T12: 0.0196 REMARK 3 T13: -0.0459 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 1.6583 L22: 2.2541 REMARK 3 L33: 2.3127 L12: 0.2694 REMARK 3 L13: 0.2510 L23: 0.2585 REMARK 3 S TENSOR REMARK 3 S11: 0.1227 S12: -0.3255 S13: -0.2581 REMARK 3 S21: 0.5162 S22: -0.0518 S23: -0.2050 REMARK 3 S31: 0.1547 S32: 0.1163 S33: -0.0709 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 131 REMARK 3 ORIGIN FOR THE GROUP (A): 221.1238 86.6199-187.2629 REMARK 3 T TENSOR REMARK 3 T11: 0.4008 T22: 0.6773 REMARK 3 T33: 0.4467 T12: -0.1897 REMARK 3 T13: -0.2847 T23: 0.1083 REMARK 3 L TENSOR REMARK 3 L11: 4.8147 L22: 3.8817 REMARK 3 L33: 3.1660 L12: 0.7892 REMARK 3 L13: 1.5278 L23: -1.5882 REMARK 3 S TENSOR REMARK 3 S11: -0.2412 S12: 1.0970 S13: 0.1647 REMARK 3 S21: -0.9287 S22: 0.2732 S23: 0.7024 REMARK 3 S31: 0.2456 S32: -0.4940 S33: -0.0320 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 132 B 321 REMARK 3 ORIGIN FOR THE GROUP (A): 244.3754 80.6404-172.0570 REMARK 3 T TENSOR REMARK 3 T11: 0.2066 T22: 0.2711 REMARK 3 T33: 0.2070 T12: -0.1413 REMARK 3 T13: 0.1246 T23: -0.1490 REMARK 3 L TENSOR REMARK 3 L11: 3.0291 L22: 1.0702 REMARK 3 L33: 1.5273 L12: 1.1999 REMARK 3 L13: -1.3577 L23: -0.1690 REMARK 3 S TENSOR REMARK 3 S11: -0.5540 S12: 0.4898 S13: -0.5509 REMARK 3 S21: -0.3772 S22: 0.1810 S23: -0.1814 REMARK 3 S31: 0.3126 S32: -0.2477 S33: 0.3729 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 322 B 426 REMARK 3 ORIGIN FOR THE GROUP (A): 233.9617 99.7435-187.7695 REMARK 3 T TENSOR REMARK 3 T11: 0.4443 T22: 0.5836 REMARK 3 T33: 0.3178 T12: -0.1123 REMARK 3 T13: -0.1873 T23: 0.2877 REMARK 3 L TENSOR REMARK 3 L11: 6.4779 L22: 5.3623 REMARK 3 L33: 3.0036 L12: 1.1984 REMARK 3 L13: -1.3027 L23: -0.2229 REMARK 3 S TENSOR REMARK 3 S11: -0.2745 S12: 1.1391 S13: 1.0267 REMARK 3 S21: -1.1137 S22: 0.4697 S23: 0.2542 REMARK 3 S31: -0.3518 S32: -0.3913 S33: -0.1952 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1001 A 1001 REMARK 3 ORIGIN FOR THE GROUP (A): 261.9554 88.8955-158.2737 REMARK 3 T TENSOR REMARK 3 T11: 0.2708 T22: 0.2674 REMARK 3 T33: 0.2719 T12: 0.0205 REMARK 3 T13: -0.0140 T23: -0.0334 REMARK 3 L TENSOR REMARK 3 L11: 16.2513 L22: 53.0374 REMARK 3 L33: 82.9569 L12: 0.6759 REMARK 3 L13: -23.3306 L23: -17.7626 REMARK 3 S TENSOR REMARK 3 S11: -0.9826 S12: 2.3170 S13: -1.4951 REMARK 3 S21: -3.0381 S22: 0.9372 S23: -1.1359 REMARK 3 S31: 2.3825 S32: -1.7399 S33: 0.0455 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1002 A 1002 REMARK 3 RESIDUE RANGE : A 1006 A 1006 REMARK 3 RESIDUE RANGE : A 1134 A 1137 REMARK 3 ORIGIN FOR THE GROUP (A): 250.3541 86.8269-157.5835 REMARK 3 T TENSOR REMARK 3 T11: 0.2518 T22: 0.2376 REMARK 3 T33: 0.2445 T12: 0.0101 REMARK 3 T13: -0.0057 T23: 0.0241 REMARK 3 L TENSOR REMARK 3 L11: 56.4850 L22: -16.9505 REMARK 3 L33: 21.9666 L12: 15.8503 REMARK 3 L13: 6.0234 L23: 56.7127 REMARK 3 S TENSOR REMARK 3 S11: 0.0204 S12: -0.9045 S13: -1.7698 REMARK 3 S21: 2.0979 S22: -0.7235 S23: -0.8945 REMARK 3 S31: 2.2962 S32: -0.0261 S33: 0.7031 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1009 A 1131 REMARK 3 RESIDUE RANGE : B 1014 B 1020 REMARK 3 ORIGIN FOR THE GROUP (A): 253.4022 96.9098-148.7598 REMARK 3 T TENSOR REMARK 3 T11: 0.1210 T22: 0.1268 REMARK 3 T33: 0.1453 T12: 0.0239 REMARK 3 T13: 0.0158 T23: -0.0329 REMARK 3 L TENSOR REMARK 3 L11: 0.6588 L22: 0.8995 REMARK 3 L33: 1.5375 L12: 0.2595 REMARK 3 L13: 0.1592 L23: 0.6974 REMARK 3 S TENSOR REMARK 3 S11: 0.0266 S12: -0.0531 S13: -0.0721 REMARK 3 S21: 0.0848 S22: 0.0053 S23: 0.0031 REMARK 3 S31: -0.0700 S32: 0.0393 S33: -0.0318 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1132 A 1133 REMARK 3 RESIDUE RANGE : B 1021 B 1062 REMARK 3 ORIGIN FOR THE GROUP (A): 243.4455 81.0272-168.6034 REMARK 3 T TENSOR REMARK 3 T11: 0.1856 T22: 0.2769 REMARK 3 T33: 0.2735 T12: -0.0708 REMARK 3 T13: 0.0929 T23: -0.1013 REMARK 3 L TENSOR REMARK 3 L11: 1.9252 L22: 0.6222 REMARK 3 L33: 1.5643 L12: 1.1428 REMARK 3 L13: -0.9095 L23: -0.1768 REMARK 3 S TENSOR REMARK 3 S11: -0.2796 S12: 0.2137 S13: -0.3477 REMARK 3 S21: -0.2604 S22: 0.0977 S23: -0.1275 REMARK 3 S31: 0.2857 S32: -0.0058 S33: 0.1820 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1063 B 1069 REMARK 3 ORIGIN FOR THE GROUP (A): 221.2914 83.3233-169.4942 REMARK 3 T TENSOR REMARK 3 T11: 0.2585 T22: 0.2590 REMARK 3 T33: 0.2571 T12: 0.0011 REMARK 3 T13: 0.0003 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 12.8485 L22: -1.2901 REMARK 3 L33: 2.5941 L12: 3.7619 REMARK 3 L13: 1.6964 L23: 1.4914 REMARK 3 S TENSOR REMARK 3 S11: 0.2914 S12: -0.2244 S13: 0.7040 REMARK 3 S21: 0.1193 S22: 0.0880 S23: 0.6574 REMARK 3 S31: 0.3175 S32: 0.1035 S33: -0.3795 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 132 A 321 REMARK 3 ORIGIN FOR THE GROUP (A): 235.9823 93.0048-157.2941 REMARK 3 T TENSOR REMARK 3 T11: 0.0131 T22: 0.1788 REMARK 3 T33: 0.1707 T12: 0.0417 REMARK 3 T13: 0.0055 T23: -0.0707 REMARK 3 L TENSOR REMARK 3 L11: 2.5237 L22: 1.7023 REMARK 3 L33: 1.9411 L12: 1.4890 REMARK 3 L13: -0.5438 L23: 0.0586 REMARK 3 S TENSOR REMARK 3 S11: -0.0372 S12: 0.0385 S13: 0.1964 REMARK 3 S21: 0.0088 S22: -0.1112 S23: 0.4114 REMARK 3 S31: -0.1299 S32: -0.4018 S33: 0.1484 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 322 A 435 REMARK 3 ORIGIN FOR THE GROUP (A): 260.9861 104.8740-152.6168 REMARK 3 T TENSOR REMARK 3 T11: 0.0864 T22: 0.1305 REMARK 3 T33: 0.0730 T12: -0.0120 REMARK 3 T13: 0.0035 T23: -0.0709 REMARK 3 L TENSOR REMARK 3 L11: 1.1031 L22: 1.8228 REMARK 3 L33: 2.8424 L12: 0.4428 REMARK 3 L13: -0.1475 L23: 0.3719 REMARK 3 S TENSOR REMARK 3 S11: 0.0112 S12: 0.0047 S13: 0.0793 REMARK 3 S21: -0.1002 S22: 0.0933 S23: -0.0574 REMARK 3 S31: -0.4138 S32: 0.2773 S33: -0.1045 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1003 B 1003 REMARK 3 ORIGIN FOR THE GROUP (A): 230.0520 97.7979-173.5059 REMARK 3 T TENSOR REMARK 3 T11: 0.2807 T22: 0.2953 REMARK 3 T33: 0.2617 T12: 0.0567 REMARK 3 T13: -0.0061 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 34.3537 L22: 1.7070 REMARK 3 L33: 15.6106 L12: -2.9296 REMARK 3 L13: 3.1110 L23: -7.0613 REMARK 3 S TENSOR REMARK 3 S11: 0.0484 S12: 1.6244 S13: -0.9954 REMARK 3 S21: -0.7065 S22: -0.1808 S23: -0.8086 REMARK 3 S31: 0.6423 S32: -0.2264 S33: 0.1324 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1004 B 1004 REMARK 3 RESIDUE RANGE : A 1005 A 1005 REMARK 3 RESIDUE RANGE : A 1007 A 1008 REMARK 3 RESIDUE RANGE : B 1005 B 1013 REMARK 3 ORIGIN FOR THE GROUP (A): 230.4586 92.2326-170.9696 REMARK 3 T TENSOR REMARK 3 T11: 0.2621 T22: 0.2706 REMARK 3 T33: 0.2714 T12: -0.0223 REMARK 3 T13: -0.0172 T23: 0.0270 REMARK 3 L TENSOR REMARK 3 L11: 10.0484 L22: -2.5451 REMARK 3 L33: -1.9837 L12: -1.1581 REMARK 3 L13: 3.7931 L23: 3.3641 REMARK 3 S TENSOR REMARK 3 S11: 0.2043 S12: 0.5621 S13: -0.1142 REMARK 3 S21: 0.6778 S22: -0.1390 S23: 0.0258 REMARK 3 S31: 0.1291 S32: -0.3402 S33: -0.0654 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1XKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030453. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.089 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45223 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 39.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.530 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1XGV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6K, MAGNESIUM CHLORIDE, SODIUM REMARK 280 CITRATE, PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.52250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.78750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.78750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 128.28375 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.78750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.78750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.76125 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.78750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.78750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 128.28375 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.78750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.78750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.76125 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 85.52250 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLN A 2 REMARK 465 VAL A 3 REMARK 465 MET A 4 REMARK 465 GLY A 115 REMARK 465 THR A 116 REMARK 465 GLY A 117 REMARK 465 TYR A 118 REMARK 465 MET B 1 REMARK 465 GLN B 2 REMARK 465 VAL B 3 REMARK 465 MET B 4 REMARK 465 ALA B 5 REMARK 465 TYR B 66 REMARK 465 GLY B 67 REMARK 465 ASN B 427 REMARK 465 GLU B 428 REMARK 465 VAL B 429 REMARK 465 LEU B 430 REMARK 465 ALA B 431 REMARK 465 GLY B 432 REMARK 465 LYS B 433 REMARK 465 ARG B 434 REMARK 465 GLY B 435 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 119 NE CZ NH1 NH2 REMARK 480 GLN A 267 CG CD OE1 NE2 REMARK 480 LYS A 433 CD CE NZ REMARK 480 SER B 15 CB OG REMARK 480 GLU B 24 CB CG CD OE1 OE2 REMARK 480 SER B 26 CB OG REMARK 480 SER B 29 CB OG REMARK 480 ARG B 70 CG CD NE CZ NH1 NH2 REMARK 480 ARG B 71 CZ NH1 NH2 REMARK 480 ARG B 84 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 86 CG CD CE NZ REMARK 480 ARG B 139 NE CZ NH1 NH2 REMARK 480 ARG B 206 CD NE CZ NH1 NH2 REMARK 480 GLU B 268 CG CD OE1 OE2 REMARK 480 LYS B 269 CD CE NZ REMARK 480 LYS B 278 CE NZ REMARK 480 GLU B 376 CB CG CD OE1 OE2 REMARK 480 LYS B 378 CB CG CD CE NZ REMARK 480 ILE B 380 CB CG1 CG2 CD1 REMARK 480 VAL B 381 CA CB CG1 CG2 REMARK 480 TYR B 383 CB CG CD1 CD2 CE1 CE2 CZ REMARK 480 TYR B 383 OH REMARK 480 LYS B 387 CB CG CD CE NZ REMARK 480 LYS B 392 CG CD CE NZ REMARK 480 LYS B 393 CB CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NH2 ARG A 139 OE2 GLU A 370 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 59 CB - CG - OD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ASP A 154 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 174 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 299 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 174 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 299 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 311 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 6 115.71 73.00 REMARK 500 ARG A 71 124.83 -170.75 REMARK 500 ARG A 103 -26.73 75.31 REMARK 500 SER A 120 122.74 54.66 REMARK 500 GLN A 143 152.10 -48.70 REMARK 500 GLU A 163 -150.50 -115.46 REMARK 500 ASP A 164 -169.52 70.26 REMARK 500 LYS A 233 56.33 -115.01 REMARK 500 THR A 240 -71.80 -112.24 REMARK 500 PHE A 256 19.31 -141.90 REMARK 500 VAL A 273 69.02 -106.97 REMARK 500 ARG A 274 118.86 -29.46 REMARK 500 GLN A 301 -83.41 -129.81 REMARK 500 ASP A 334 -74.54 -57.05 REMARK 500 ALA A 346 58.37 36.17 REMARK 500 SER B 15 91.03 -170.69 REMARK 500 PRO B 17 161.76 -49.27 REMARK 500 ASP B 34 -1.19 60.76 REMARK 500 SER B 69 -16.90 -46.11 REMARK 500 ARG B 71 132.20 -178.36 REMARK 500 ARG B 103 -20.43 70.70 REMARK 500 GLU B 163 -144.64 -124.17 REMARK 500 ASP B 164 -168.72 67.33 REMARK 500 MET B 237 79.69 -104.78 REMARK 500 PHE B 256 28.57 -140.48 REMARK 500 GLN B 264 32.35 -79.06 REMARK 500 GLU B 265 -50.36 -158.39 REMARK 500 GLU B 268 -47.88 178.69 REMARK 500 ARG B 296 52.24 -145.22 REMARK 500 GLN B 301 -82.36 -132.66 REMARK 500 ASP B 334 92.89 -65.79 REMARK 500 ALA B 346 67.37 30.91 REMARK 500 ALA B 350 -75.82 -37.63 REMARK 500 GLN B 390 24.12 -70.04 REMARK 500 HIS B 401 30.45 -82.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 335 ILE A 336 -149.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1005 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 287 OD2 REMARK 620 2 ASP B 311 OD2 96.5 REMARK 620 3 ICT B1004 O2 152.1 93.0 REMARK 620 4 ICT B1004 O7 80.2 96.9 72.6 REMARK 620 5 HOH B1005 O 79.0 175.5 91.0 82.3 REMARK 620 6 HOH B1006 O 97.8 93.7 107.7 169.4 87.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1006 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 311 OD2 REMARK 620 2 ASP A 315 OD1 105.0 REMARK 620 3 ICT A1002 O2 84.0 144.5 REMARK 620 4 ICT A1002 O7 90.4 151.8 59.1 REMARK 620 5 HOH A1135 O 145.6 74.5 79.1 105.8 REMARK 620 6 HOH A1136 O 150.8 94.8 92.2 63.4 60.2 REMARK 620 7 HOH A1137 O 69.0 66.5 86.0 141.7 80.1 139.8 REMARK 620 8 ASP B 287 OD2 94.6 74.4 140.0 81.0 117.4 70.1 130.7 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP B 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT B 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TYO RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE FROM AEROPYRUM PERNIX IN COMPLEX WITH REMARK 900 ETHENO-NADP REMARK 900 RELATED ID: 1XGV RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE FROM AEROPYRUM PERNIX DBREF 1XKD A 1 435 UNP Q9YE81 Q9YE81_AERPE 1 435 DBREF 1XKD B 1 435 UNP Q9YE81 Q9YE81_AERPE 1 435 SEQRES 1 A 435 MET GLN VAL MET ALA SER PRO PRO CYS THR THR GLU GLU SEQRES 2 A 435 LEU SER PRO PRO PRO GLY GLY SER LEU VAL GLU TYR SER SEQRES 3 A 435 GLY GLY SER LEU ARG VAL PRO ASP ASN PRO VAL VAL ALA SEQRES 4 A 435 PHE ILE ARG GLY ASP GLY VAL GLY PRO GLU VAL VAL GLU SEQRES 5 A 435 SER ALA LEU LYS VAL VAL ASP ALA ALA VAL LYS LYS VAL SEQRES 6 A 435 TYR GLY GLY SER ARG ARG ILE VAL TRP TRP GLU LEU LEU SEQRES 7 A 435 ALA GLY HIS LEU ALA ARG GLU LYS CYS GLY GLU LEU LEU SEQRES 8 A 435 PRO LYS ALA THR LEU GLU GLY ILE ARG LEU ALA ARG VAL SEQRES 9 A 435 ALA LEU LYS GLY PRO LEU GLU THR PRO VAL GLY THR GLY SEQRES 10 A 435 TYR ARG SER LEU ASN VAL ALA ILE ARG GLN ALA LEU ASP SEQRES 11 A 435 LEU TYR ALA ASN ILE ARG PRO VAL ARG TYR TYR GLY GLN SEQRES 12 A 435 PRO ALA PRO HIS LYS TYR ALA ASP ARG VAL ASP MET VAL SEQRES 13 A 435 ILE PHE ARG GLU ASN THR GLU ASP VAL TYR ALA GLY ILE SEQRES 14 A 435 GLU TRP PRO HIS ASP SER PRO GLU ALA ALA ARG ILE ARG SEQRES 15 A 435 ARG PHE LEU ALA GLU GLU PHE GLY ILE SER ILE ARG GLU SEQRES 16 A 435 ASP ALA GLY ILE GLY VAL LYS PRO ILE SER ARG PHE ALA SEQRES 17 A 435 THR ARG ARG LEU MET GLU ARG ALA LEU GLU TRP ALA LEU SEQRES 18 A 435 ARG ASN GLY ASN THR VAL VAL THR ILE MET HIS LYS GLY SEQRES 19 A 435 ASN ILE MET LYS TYR THR GLU GLY ALA PHE MET ARG TRP SEQRES 20 A 435 ALA TYR GLU VAL ALA LEU GLU LYS PHE ARG GLU HIS VAL SEQRES 21 A 435 VAL THR GLU GLN GLU VAL GLN GLU LYS TYR GLY GLY VAL SEQRES 22 A 435 ARG PRO GLU GLY LYS ILE LEU VAL ASN ASP ARG ILE ALA SEQRES 23 A 435 ASP ASN MET LEU GLN GLN ILE ILE THR ARG PRO TRP ASP SEQRES 24 A 435 TYR GLN VAL ILE VAL ALA PRO ASN LEU ASN GLY ASP TYR SEQRES 25 A 435 ILE SER ASP ALA ALA SER ALA LEU VAL GLY GLY ILE GLY SEQRES 26 A 435 MET ALA ALA GLY MET ASN MET GLY ASP GLY ILE ALA VAL SEQRES 27 A 435 ALA GLU PRO VAL HIS GLY THR ALA PRO LYS TYR ALA GLY SEQRES 28 A 435 LYS ASP LEU ILE ASN PRO SER ALA GLU ILE LEU SER ALA SEQRES 29 A 435 SER LEU LEU ILE GLY GLU PHE MET GLY TRP ARG GLU VAL SEQRES 30 A 435 LYS SER ILE VAL GLU TYR ALA ILE ARG LYS ALA VAL GLN SEQRES 31 A 435 SER LYS LYS VAL THR GLN ASP LEU ALA ARG HIS MET PRO SEQRES 32 A 435 GLY VAL GLN PRO LEU ARG THR SER GLU TYR THR GLU THR SEQRES 33 A 435 LEU ILE ALA TYR ILE ASP GLU ALA ASP LEU ASN GLU VAL SEQRES 34 A 435 LEU ALA GLY LYS ARG GLY SEQRES 1 B 435 MET GLN VAL MET ALA SER PRO PRO CYS THR THR GLU GLU SEQRES 2 B 435 LEU SER PRO PRO PRO GLY GLY SER LEU VAL GLU TYR SER SEQRES 3 B 435 GLY GLY SER LEU ARG VAL PRO ASP ASN PRO VAL VAL ALA SEQRES 4 B 435 PHE ILE ARG GLY ASP GLY VAL GLY PRO GLU VAL VAL GLU SEQRES 5 B 435 SER ALA LEU LYS VAL VAL ASP ALA ALA VAL LYS LYS VAL SEQRES 6 B 435 TYR GLY GLY SER ARG ARG ILE VAL TRP TRP GLU LEU LEU SEQRES 7 B 435 ALA GLY HIS LEU ALA ARG GLU LYS CYS GLY GLU LEU LEU SEQRES 8 B 435 PRO LYS ALA THR LEU GLU GLY ILE ARG LEU ALA ARG VAL SEQRES 9 B 435 ALA LEU LYS GLY PRO LEU GLU THR PRO VAL GLY THR GLY SEQRES 10 B 435 TYR ARG SER LEU ASN VAL ALA ILE ARG GLN ALA LEU ASP SEQRES 11 B 435 LEU TYR ALA ASN ILE ARG PRO VAL ARG TYR TYR GLY GLN SEQRES 12 B 435 PRO ALA PRO HIS LYS TYR ALA ASP ARG VAL ASP MET VAL SEQRES 13 B 435 ILE PHE ARG GLU ASN THR GLU ASP VAL TYR ALA GLY ILE SEQRES 14 B 435 GLU TRP PRO HIS ASP SER PRO GLU ALA ALA ARG ILE ARG SEQRES 15 B 435 ARG PHE LEU ALA GLU GLU PHE GLY ILE SER ILE ARG GLU SEQRES 16 B 435 ASP ALA GLY ILE GLY VAL LYS PRO ILE SER ARG PHE ALA SEQRES 17 B 435 THR ARG ARG LEU MET GLU ARG ALA LEU GLU TRP ALA LEU SEQRES 18 B 435 ARG ASN GLY ASN THR VAL VAL THR ILE MET HIS LYS GLY SEQRES 19 B 435 ASN ILE MET LYS TYR THR GLU GLY ALA PHE MET ARG TRP SEQRES 20 B 435 ALA TYR GLU VAL ALA LEU GLU LYS PHE ARG GLU HIS VAL SEQRES 21 B 435 VAL THR GLU GLN GLU VAL GLN GLU LYS TYR GLY GLY VAL SEQRES 22 B 435 ARG PRO GLU GLY LYS ILE LEU VAL ASN ASP ARG ILE ALA SEQRES 23 B 435 ASP ASN MET LEU GLN GLN ILE ILE THR ARG PRO TRP ASP SEQRES 24 B 435 TYR GLN VAL ILE VAL ALA PRO ASN LEU ASN GLY ASP TYR SEQRES 25 B 435 ILE SER ASP ALA ALA SER ALA LEU VAL GLY GLY ILE GLY SEQRES 26 B 435 MET ALA ALA GLY MET ASN MET GLY ASP GLY ILE ALA VAL SEQRES 27 B 435 ALA GLU PRO VAL HIS GLY THR ALA PRO LYS TYR ALA GLY SEQRES 28 B 435 LYS ASP LEU ILE ASN PRO SER ALA GLU ILE LEU SER ALA SEQRES 29 B 435 SER LEU LEU ILE GLY GLU PHE MET GLY TRP ARG GLU VAL SEQRES 30 B 435 LYS SER ILE VAL GLU TYR ALA ILE ARG LYS ALA VAL GLN SEQRES 31 B 435 SER LYS LYS VAL THR GLN ASP LEU ALA ARG HIS MET PRO SEQRES 32 B 435 GLY VAL GLN PRO LEU ARG THR SER GLU TYR THR GLU THR SEQRES 33 B 435 LEU ILE ALA TYR ILE ASP GLU ALA ASP LEU ASN GLU VAL SEQRES 34 B 435 LEU ALA GLY LYS ARG GLY HET CA A1005 1 HET CA A1006 1 HET NAP A1001 48 HET ICT A1002 13 HET NAP B1003 48 HET ICT B1004 13 HETNAM CA CALCIUM ION HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM ICT ISOCITRIC ACID HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 CA 2(CA 2+) FORMUL 5 NAP 2(C21 H28 N7 O17 P3) FORMUL 6 ICT 2(C6 H8 O7) FORMUL 9 HOH *196(H2 O) HELIX 1 1 THR A 10 LEU A 14 5 5 HELIX 2 2 VAL A 46 GLY A 67 1 22 HELIX 3 3 GLY A 80 GLY A 88 1 9 HELIX 4 4 PRO A 92 ARG A 103 1 12 HELIX 5 5 SER A 120 ASP A 130 1 11 HELIX 6 6 TYR A 149 VAL A 153 5 5 HELIX 7 7 GLU A 163 GLY A 168 5 6 HELIX 8 8 SER A 175 GLY A 190 1 16 HELIX 9 9 ARG A 206 GLY A 224 1 19 HELIX 10 10 THR A 240 PHE A 256 1 17 HELIX 11 11 GLU A 263 LYS A 269 1 7 HELIX 12 12 ALA A 286 ARG A 296 1 11 HELIX 13 13 PRO A 297 TYR A 300 5 4 HELIX 14 14 PRO A 306 VAL A 321 1 16 HELIX 15 15 GLY A 323 MET A 326 5 4 HELIX 16 16 ALA A 346 ALA A 350 5 5 HELIX 17 17 PRO A 357 GLU A 370 1 14 HELIX 18 18 TRP A 374 SER A 391 1 18 HELIX 19 19 THR A 395 ARG A 400 1 6 HELIX 20 20 ARG A 409 ALA A 424 1 16 HELIX 21 21 ASP A 425 LEU A 430 1 6 HELIX 22 22 VAL B 46 VAL B 62 1 17 HELIX 23 23 GLY B 80 CYS B 87 1 8 HELIX 24 24 PRO B 92 ARG B 103 1 12 HELIX 25 25 SER B 120 LEU B 129 1 10 HELIX 26 26 TYR B 149 VAL B 153 5 5 HELIX 27 27 GLU B 163 GLY B 168 5 6 HELIX 28 28 SER B 175 GLY B 190 1 16 HELIX 29 29 ARG B 206 GLY B 224 1 19 HELIX 30 30 THR B 240 PHE B 256 1 17 HELIX 31 31 GLU B 263 GLN B 267 1 5 HELIX 32 32 ALA B 286 ARG B 296 1 11 HELIX 33 33 PRO B 297 TYR B 300 5 4 HELIX 34 34 PRO B 306 VAL B 321 1 16 HELIX 35 35 GLY B 323 ALA B 327 5 5 HELIX 36 36 ALA B 346 ALA B 350 5 5 HELIX 37 37 PRO B 357 PHE B 371 1 15 HELIX 38 38 TRP B 374 GLN B 390 1 17 HELIX 39 39 THR B 395 ARG B 400 1 6 HELIX 40 40 ARG B 409 GLU B 423 1 15 SHEET 1 A 2 GLU A 24 SER A 26 0 SHEET 2 A 2 SER A 29 ARG A 31 -1 O ARG A 31 N GLU A 24 SHEET 1 B11 VAL A 73 LEU A 77 0 SHEET 2 B11 VAL A 37 ILE A 41 1 N PHE A 40 O LEU A 77 SHEET 3 B11 VAL A 104 LYS A 107 1 O LEU A 106 N ALA A 39 SHEET 4 B11 ALA A 337 PRO A 341 1 O ALA A 339 N ALA A 105 SHEET 5 B11 ALA A 328 MET A 332 -1 N ASN A 331 O VAL A 338 SHEET 6 B11 ALA A 133 VAL A 138 -1 N ILE A 135 O MET A 330 SHEET 7 B11 MET A 155 GLU A 160 -1 O MET A 155 N VAL A 138 SHEET 8 B11 VAL A 302 ALA A 305 1 O ILE A 303 N PHE A 158 SHEET 9 B11 VAL A 227 HIS A 232 1 N THR A 229 O VAL A 304 SHEET 10 B11 ILE A 279 ILE A 285 1 O LEU A 280 N VAL A 228 SHEET 11 B11 VAL A 260 THR A 262 1 N VAL A 261 O VAL A 281 SHEET 1 C 4 GLU A 170 TRP A 171 0 SHEET 2 C 4 ALA A 197 SER A 205 -1 O ILE A 199 N TRP A 171 SHEET 3 C 4 ALA B 197 SER B 205 -1 O LYS B 202 N GLY A 200 SHEET 4 C 4 GLU B 170 TRP B 171 -1 N TRP B 171 O ILE B 199 SHEET 1 D 3 SER B 21 LEU B 22 0 SHEET 2 D 3 PRO B 36 ILE B 41 1 O VAL B 37 N SER B 21 SHEET 3 D 3 VAL B 73 GLU B 76 1 O TRP B 75 N PHE B 40 SHEET 1 E11 SER B 21 LEU B 22 0 SHEET 2 E11 PRO B 36 ILE B 41 1 O VAL B 37 N SER B 21 SHEET 3 E11 VAL B 104 LYS B 107 1 O LEU B 106 N ALA B 39 SHEET 4 E11 ILE B 336 ALA B 339 1 O ALA B 339 N LYS B 107 SHEET 5 E11 MET B 330 GLY B 333 -1 N GLY B 333 O ILE B 336 SHEET 6 E11 ALA B 133 VAL B 138 -1 N ALA B 133 O MET B 332 SHEET 7 E11 MET B 155 GLU B 160 -1 O MET B 155 N VAL B 138 SHEET 8 E11 VAL B 302 ALA B 305 1 O ILE B 303 N PHE B 158 SHEET 9 E11 VAL B 227 HIS B 232 1 N THR B 229 O VAL B 304 SHEET 10 E11 ILE B 279 ILE B 285 1 O LEU B 280 N VAL B 228 SHEET 11 E11 VAL B 260 THR B 262 1 N VAL B 261 O VAL B 281 SHEET 1 F 2 GLU B 24 SER B 26 0 SHEET 2 F 2 SER B 29 ARG B 31 -1 O ARG B 31 N GLU B 24 SSBOND 1 CYS A 9 CYS A 87 1555 1555 2.03 SSBOND 2 CYS B 9 CYS B 87 1555 1555 2.03 LINK OD2 ASP A 287 CA CA A1005 1555 1555 2.33 LINK OD2 ASP A 311 CA CA A1006 1555 1555 2.23 LINK OD1 ASP A 315 CA CA A1006 1555 1555 2.40 LINK O2 ICT A1002 CA CA A1006 1555 1555 2.64 LINK O7 ICT A1002 CA CA A1006 1555 1555 2.36 LINK CA CA A1005 OD2 ASP B 311 1555 1555 2.06 LINK CA CA A1005 O2 ICT B1004 1555 1555 2.28 LINK CA CA A1005 O7 ICT B1004 1555 1555 2.27 LINK CA CA A1005 O HOH B1005 1555 1555 2.36 LINK CA CA A1005 O HOH B1006 1555 1555 2.10 LINK CA CA A1006 O HOH A1135 1555 1555 2.71 LINK CA CA A1006 O HOH A1136 1555 1555 2.57 LINK CA CA A1006 O HOH A1137 1555 1555 2.54 LINK CA CA A1006 OD2 ASP B 287 1555 1555 2.28 SITE 1 AC1 5 ASP A 287 ASP B 311 ICT B1004 HOH B1005 SITE 2 AC1 5 HOH B1006 SITE 1 AC2 7 ASP A 311 ASP A 315 ICT A1002 HOH A1135 SITE 2 AC2 7 HOH A1136 HOH A1137 ASP B 287 SITE 1 AC3 18 LYS A 107 PRO A 109 LEU A 110 THR A 112 SITE 2 AC3 18 ASN A 122 GLY A 325 GLU A 340 PRO A 341 SITE 3 AC3 18 VAL A 342 HIS A 343 GLY A 344 THR A 345 SITE 4 AC3 18 ALA A 346 TYR A 349 ILE A 355 ASN A 356 SITE 5 AC3 18 ASP A 397 ARG A 400 SITE 1 AC4 9 ARG A 136 ARG A 159 TYR A 166 ASP A 311 SITE 2 AC4 9 CA A1006 HOH A1136 LYS B 233 ASN B 235 SITE 3 AC4 9 ASP B 287 SITE 1 AC5 28 ASN A 235 ILE A 285 ASN A 288 GLN A 291 SITE 2 AC5 28 GLN A 292 ARG A 296 PRO B 109 LEU B 110 SITE 3 AC5 28 THR B 112 ASN B 122 ARG B 126 ILE B 324 SITE 4 AC5 28 GLY B 325 GLU B 340 VAL B 342 HIS B 343 SITE 5 AC5 28 GLY B 344 THR B 345 ALA B 346 LYS B 348 SITE 6 AC5 28 TYR B 349 ILE B 355 ASN B 356 ASP B 397 SITE 7 AC5 28 ICT B1004 HOH B1008 HOH B1009 HOH B1010 SITE 1 AC6 14 LYS A 233 ASP A 287 CA A1005 THR B 112 SITE 2 AC6 14 SER B 120 ASN B 122 ARG B 126 ARG B 136 SITE 3 AC6 14 ARG B 159 TYR B 166 ASP B 311 NAP B1003 SITE 4 AC6 14 HOH B1005 HOH B1007 CRYST1 107.575 107.575 171.045 90.00 90.00 90.00 P 43 21 2 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009296 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009296 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005846 0.00000