HEADER TRANSFERASE 26-JUN-08 3DKV TITLE CRYSTAL STRUCTURE OF ADENYLATE KINASE VARIANT AKLSE1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENYLATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ATP-AMP TRANSPHOSPHORYLASE, AK, SUPEROXIDE-INDUCIBLE PROTEIN COMPND 5 16, SOI16; COMPND 6 EC: 2.7.4.3; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: ADK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS PHOSPHOTRANSFERASE, ZINC COORDINATION, ATP-BINDING, KINASE, METAL- KEYWDS 2 BINDING, NUCLEOTIDE BIOSYNTHESIS, NUCLEOTIDE-BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.M.BANNEN,C.M.BIANCHETTI,C.A.BINGMAN,E.B.BITTO REVDAT 5 30-AUG-23 3DKV 1 REMARK LINK REVDAT 4 25-OCT-17 3DKV 1 REMARK REVDAT 3 24-OCT-12 3DKV 1 REVDAT 2 13-JUL-11 3DKV 1 VERSN REVDAT 1 09-JUN-09 3DKV 0 JRNL AUTH R.M.BANNEN,E.BAE,J.G.MCCOY,G.N.PHILLIPS JR. JRNL TITL CRYSTAL STRUCTURE OF ADENYLATE KINASE VARIANT AKLSE1. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22301 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1145 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) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1518 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 98 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1687 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.40000 REMARK 3 B22 (A**2) : -0.69000 REMARK 3 B33 (A**2) : 0.29000 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): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.765 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1786 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2419 ; 1.582 ; 2.040 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 218 ; 5.332 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;36.689 ;25.190 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 322 ;12.994 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;13.723 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 277 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1304 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 863 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1236 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 157 ; 0.144 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 33 ; 0.242 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.187 ; 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): 1118 ; 0.775 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1743 ; 1.067 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 759 ; 1.917 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 675 ; 2.852 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 15 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 1 A 9 REMARK 3 ORIGIN FOR THE GROUP (A): -13.2403 -12.2159 -13.3579 REMARK 3 T TENSOR REMARK 3 T11: -0.0149 T22: -0.0214 REMARK 3 T33: 0.0100 T12: 0.0031 REMARK 3 T13: -0.0204 T23: -0.0092 REMARK 3 L TENSOR REMARK 3 L11: 4.3815 L22: 3.7410 REMARK 3 L33: 7.2286 L12: 1.1340 REMARK 3 L13: -0.9791 L23: -3.1511 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: 0.1090 S13: -0.0273 REMARK 3 S21: -0.2732 S22: -0.1767 S23: -0.0561 REMARK 3 S31: 0.0911 S32: 0.3316 S33: 0.1609 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 : A 10 A 23 REMARK 3 ORIGIN FOR THE GROUP (A): -21.6208 -7.0756 -11.5173 REMARK 3 T TENSOR REMARK 3 T11: 0.0374 T22: 0.0594 REMARK 3 T33: 0.0550 T12: -0.0008 REMARK 3 T13: -0.0256 T23: 0.0182 REMARK 3 L TENSOR REMARK 3 L11: 2.7889 L22: 6.1136 REMARK 3 L33: 8.9568 L12: 3.2574 REMARK 3 L13: -4.1300 L23: -5.2901 REMARK 3 S TENSOR REMARK 3 S11: 0.0258 S12: 0.0044 S13: 0.1059 REMARK 3 S21: 0.0735 S22: 0.0561 S23: 0.2085 REMARK 3 S31: -0.4676 S32: -0.0720 S33: -0.0819 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 : A 24 A 38 REMARK 3 ORIGIN FOR THE GROUP (A): -12.5093 -4.7395 -5.0280 REMARK 3 T TENSOR REMARK 3 T11: 0.1080 T22: 0.0372 REMARK 3 T33: 0.1068 T12: -0.0291 REMARK 3 T13: -0.0713 T23: 0.0178 REMARK 3 L TENSOR REMARK 3 L11: 4.3680 L22: 1.7455 REMARK 3 L33: 2.2935 L12: 2.1311 REMARK 3 L13: 0.0943 L23: -0.9423 REMARK 3 S TENSOR REMARK 3 S11: -0.2321 S12: -0.2164 S13: 0.1954 REMARK 3 S21: -0.0192 S22: -0.0930 S23: -0.0673 REMARK 3 S31: -0.5227 S32: 0.1041 S33: 0.3251 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 : A 39 A 49 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6072 6.4488 -1.8002 REMARK 3 T TENSOR REMARK 3 T11: 0.5379 T22: 0.1590 REMARK 3 T33: 0.2740 T12: -0.2678 REMARK 3 T13: -0.2613 T23: 0.0643 REMARK 3 L TENSOR REMARK 3 L11: 17.3787 L22: 15.4757 REMARK 3 L33: 19.0709 L12: -2.4091 REMARK 3 L13: -1.1681 L23: 3.2177 REMARK 3 S TENSOR REMARK 3 S11: -0.2358 S12: -0.7682 S13: 0.8121 REMARK 3 S21: 1.1711 S22: -0.3407 S23: -0.5416 REMARK 3 S31: -1.3660 S32: 0.4158 S33: 0.5766 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 50 A 61 REMARK 3 ORIGIN FOR THE GROUP (A): 0.7619 2.7310 -12.5273 REMARK 3 T TENSOR REMARK 3 T11: 0.1887 T22: 0.2400 REMARK 3 T33: 0.2886 T12: -0.2273 REMARK 3 T13: -0.1368 T23: 0.1738 REMARK 3 L TENSOR REMARK 3 L11: 5.1462 L22: 11.4452 REMARK 3 L33: 5.4173 L12: -5.6199 REMARK 3 L13: 1.1659 L23: -5.2899 REMARK 3 S TENSOR REMARK 3 S11: -0.3468 S12: 0.4254 S13: 0.6376 REMARK 3 S21: 0.2956 S22: -0.3062 S23: -0.7032 REMARK 3 S31: -0.8682 S32: 0.8596 S33: 0.6530 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 62 A 76 REMARK 3 ORIGIN FOR THE GROUP (A): -4.3918 -9.7447 -0.2159 REMARK 3 T TENSOR REMARK 3 T11: 0.0379 T22: 0.0651 REMARK 3 T33: 0.0988 T12: -0.0140 REMARK 3 T13: -0.0604 T23: 0.0211 REMARK 3 L TENSOR REMARK 3 L11: 6.5256 L22: 2.8229 REMARK 3 L33: 7.9971 L12: 0.1311 REMARK 3 L13: 0.7593 L23: -1.8476 REMARK 3 S TENSOR REMARK 3 S11: -0.3682 S12: -0.0606 S13: 0.3771 REMARK 3 S21: 0.1788 S22: 0.0125 S23: -0.0374 REMARK 3 S31: -0.4223 S32: -0.0321 S33: 0.3557 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 77 A 85 REMARK 3 ORIGIN FOR THE GROUP (A): -13.7954 -13.5936 -3.4875 REMARK 3 T TENSOR REMARK 3 T11: 0.0219 T22: 0.0913 REMARK 3 T33: 0.0702 T12: 0.0014 REMARK 3 T13: -0.0075 T23: 0.0224 REMARK 3 L TENSOR REMARK 3 L11: 9.1233 L22: 3.8416 REMARK 3 L33: 5.9606 L12: 1.5134 REMARK 3 L13: -0.8123 L23: -2.3757 REMARK 3 S TENSOR REMARK 3 S11: -0.1206 S12: -0.6350 S13: -0.2149 REMARK 3 S21: 0.0111 S22: 0.0532 S23: -0.0352 REMARK 3 S31: -0.0188 S32: 0.0305 S33: 0.0675 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 86 A 100 REMARK 3 ORIGIN FOR THE GROUP (A): -1.9690 -14.6074 -10.2036 REMARK 3 T TENSOR REMARK 3 T11: -0.0086 T22: 0.1711 REMARK 3 T33: 0.0904 T12: -0.0050 REMARK 3 T13: 0.0047 T23: 0.0307 REMARK 3 L TENSOR REMARK 3 L11: 1.1186 L22: 6.0666 REMARK 3 L33: 5.9368 L12: -1.2524 REMARK 3 L13: 1.5083 L23: -2.8621 REMARK 3 S TENSOR REMARK 3 S11: 0.0429 S12: 0.4851 S13: 0.0605 REMARK 3 S21: -0.2994 S22: -0.2214 S23: -0.3155 REMARK 3 S31: -0.0602 S32: 0.6285 S33: 0.1785 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 : A 101 A 115 REMARK 3 ORIGIN FOR THE GROUP (A): -11.0354 -18.0188 -11.0487 REMARK 3 T TENSOR REMARK 3 T11: 0.0292 T22: 0.0412 REMARK 3 T33: 0.0719 T12: -0.0091 REMARK 3 T13: 0.0219 T23: 0.0118 REMARK 3 L TENSOR REMARK 3 L11: 2.5241 L22: 2.1645 REMARK 3 L33: 4.9733 L12: -1.4080 REMARK 3 L13: 3.3362 L23: -0.9793 REMARK 3 S TENSOR REMARK 3 S11: 0.1532 S12: 0.0386 S13: -0.1134 REMARK 3 S21: -0.1561 S22: -0.0511 S23: -0.0687 REMARK 3 S31: 0.1941 S32: 0.2585 S33: -0.1021 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 116 A 127 REMARK 3 ORIGIN FOR THE GROUP (A): -15.6707 2.2951 -25.0017 REMARK 3 T TENSOR REMARK 3 T11: 0.1168 T22: 0.0685 REMARK 3 T33: 0.0609 T12: -0.0209 REMARK 3 T13: -0.0316 T23: 0.0474 REMARK 3 L TENSOR REMARK 3 L11: 4.2066 L22: 9.3437 REMARK 3 L33: 10.1767 L12: -2.2773 REMARK 3 L13: -2.1591 L23: -4.9917 REMARK 3 S TENSOR REMARK 3 S11: -0.0276 S12: 0.3784 S13: 0.0857 REMARK 3 S21: -0.4395 S22: -0.2250 S23: -0.2696 REMARK 3 S31: 0.3366 S32: 0.0953 S33: 0.2527 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 128 A 156 REMARK 3 ORIGIN FOR THE GROUP (A): -25.2218 7.3566 -11.8055 REMARK 3 T TENSOR REMARK 3 T11: 0.3207 T22: 0.0888 REMARK 3 T33: 0.0489 T12: 0.1145 REMARK 3 T13: -0.0078 T23: 0.0162 REMARK 3 L TENSOR REMARK 3 L11: 3.4596 L22: 1.8397 REMARK 3 L33: 6.8862 L12: -0.3547 REMARK 3 L13: 0.4885 L23: 0.1886 REMARK 3 S TENSOR REMARK 3 S11: -0.0969 S12: -0.3972 S13: 0.2261 REMARK 3 S21: 0.4356 S22: 0.1830 S23: 0.0537 REMARK 3 S31: -0.6800 S32: -0.4586 S33: -0.0862 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 : A 157 A 178 REMARK 3 ORIGIN FOR THE GROUP (A): -7.7850 4.4727 -19.6110 REMARK 3 T TENSOR REMARK 3 T11: 0.1568 T22: 0.1188 REMARK 3 T33: 0.1912 T12: -0.1119 REMARK 3 T13: -0.0780 T23: 0.1247 REMARK 3 L TENSOR REMARK 3 L11: 3.3660 L22: 4.4347 REMARK 3 L33: 3.8841 L12: -2.7116 REMARK 3 L13: -1.1194 L23: 0.3848 REMARK 3 S TENSOR REMARK 3 S11: -0.0097 S12: 0.2897 S13: 0.6693 REMARK 3 S21: -0.0165 S22: -0.2190 S23: -0.5953 REMARK 3 S31: -0.5252 S32: 0.3289 S33: 0.2287 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 179 A 188 REMARK 3 ORIGIN FOR THE GROUP (A): -4.6379 -17.3979 -20.3625 REMARK 3 T TENSOR REMARK 3 T11: 0.2572 T22: 0.2421 REMARK 3 T33: 0.0586 T12: 0.1073 REMARK 3 T13: 0.0639 T23: -0.0292 REMARK 3 L TENSOR REMARK 3 L11: 11.4079 L22: 8.2500 REMARK 3 L33: 12.6101 L12: 2.4870 REMARK 3 L13: -1.6844 L23: -10.1283 REMARK 3 S TENSOR REMARK 3 S11: 0.0394 S12: 0.5721 S13: -0.1974 REMARK 3 S21: -0.9611 S22: -0.0721 S23: -0.2621 REMARK 3 S31: 1.0711 S32: 0.7018 S33: 0.0327 REMARK 3 REMARK 3 TLS GROUP : 14 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 189 A 202 REMARK 3 ORIGIN FOR THE GROUP (A): -18.5648 -13.7919 -20.9196 REMARK 3 T TENSOR REMARK 3 T11: 0.1518 T22: 0.0399 REMARK 3 T33: 0.0408 T12: -0.0560 REMARK 3 T13: -0.0387 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 6.0428 L22: 6.5667 REMARK 3 L33: 5.6170 L12: -3.1544 REMARK 3 L13: 3.1714 L23: -2.1299 REMARK 3 S TENSOR REMARK 3 S11: 0.2237 S12: 0.3585 S13: -0.2591 REMARK 3 S21: -0.7187 S22: -0.0956 S23: 0.2393 REMARK 3 S31: 0.4049 S32: 0.1648 S33: -0.1280 REMARK 3 REMARK 3 TLS GROUP : 15 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 203 A 217 REMARK 3 ORIGIN FOR THE GROUP (A): -24.3661 -17.9528 -13.6886 REMARK 3 T TENSOR REMARK 3 T11: 0.0306 T22: 0.0835 REMARK 3 T33: 0.1016 T12: -0.0511 REMARK 3 T13: -0.0273 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 5.2877 L22: 11.1731 REMARK 3 L33: 9.0427 L12: -4.3356 REMARK 3 L13: 3.3631 L23: -6.2919 REMARK 3 S TENSOR REMARK 3 S11: -0.1141 S12: -0.0187 S13: -0.4122 REMARK 3 S21: 0.1190 S22: 0.3259 S23: 0.6446 REMARK 3 S31: 0.2233 S32: -0.3083 S33: -0.2118 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3DKV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048164. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97297 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26423 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.690 REMARK 200 RESOLUTION RANGE LOW (A) : 50.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1AKY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4000, 400MM NACL, 100 MM NA REMARK 280 ACETATE, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 22.31200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.49750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.02800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.49750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.31200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.02800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 O HOH A 228 O HOH A 396 2.19 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 ASN A 142 60.57 -159.71 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 ZN A 218 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 130 SG REMARK 620 2 CYS A 133 SG 103.5 REMARK 620 3 CYS A 150 SG 106.1 116.8 REMARK 620 4 ASP A 153 OD2 112.0 102.3 115.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 219 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 AP5 A 220 O2B REMARK 620 2 AP5 A 220 O2G 80.4 REMARK 620 3 EDO A 223 O1 121.4 158.2 REMARK 620 4 EDO A 223 O2 161.6 85.0 73.9 REMARK 620 5 HOH A 227 O 90.0 99.0 83.2 81.3 REMARK 620 6 HOH A 238 O 91.4 94.3 84.8 100.8 166.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AP5 A 220 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 222 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 223 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DL0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ADENYLATE KINASE VARIANT AKLSE3 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE GENE WAS SYNTHESIZED BY DE NOVO SYNTHESIS. MUTATIONS REMARK 999 WERE MADE TO AN ADENYLATE KINASE SEQUENCE FROM BACILLUS REMARK 999 SUBTILIS TO OPTIMIZE THE PROTEIN'S STRUCTURAL ENTROPY. DBREF 3DKV A 1 217 UNP P16304 KAD_BACSU 1 217 SEQADV 3DKV ILE A 3 UNP P16304 LEU 3 SEE REMARK 999 SEQADV 3DKV ALA A 17 UNP P16304 GLY 17 SEE REMARK 999 SEQADV 3DKV LYS A 23 UNP P16304 ASP 23 SEE REMARK 999 SEQADV 3DKV ARG A 69 UNP P16304 LYS 69 SEE REMARK 999 SEQADV 3DKV SER A 73 UNP P16304 GLY 73 SEE REMARK 999 SEQADV 3DKV SER A 75 UNP P16304 ASP 75 SEE REMARK 999 SEQADV 3DKV MET A 103 UNP P16304 TYR 103 SEE REMARK 999 SEQADV 3DKV ARG A 105 UNP P16304 LYS 105 SEE REMARK 999 SEQADV 3DKV GLN A 114 UNP P16304 GLU 114 SEE REMARK 999 SEQADV 3DKV GLU A 118 UNP P16304 ASP 118 SEE REMARK 999 SEQADV 3DKV GLU A 119 UNP P16304 VAL 119 SEE REMARK 999 SEQADV 3DKV THR A 169 UNP P16304 SER 169 SEE REMARK 999 SEQADV 3DKV ALA A 180 UNP P16304 GLN 180 SEE REMARK 999 SEQADV 3DKV ALA A 184 UNP P16304 ASP 184 SEE REMARK 999 SEQADV 3DKV ASP A 187 UNP P16304 SER 187 SEE REMARK 999 SEQADV 3DKV SER A 188 UNP P16304 GLU 188 SEE REMARK 999 SEQADV 3DKV GLU A 190 UNP P16304 GLY 190 SEE REMARK 999 SEQADV 3DKV VAL A 191 UNP P16304 TYR 191 SEE REMARK 999 SEQADV 3DKV VAL A 193 UNP P16304 ALA 193 SEE REMARK 999 SEQADV 3DKV PHE A 205 UNP P16304 TYR 205 SEE REMARK 999 SEQADV 3DKV VAL A 210 UNP P16304 ASP 210 SEE REMARK 999 SEQADV 3DKV ILE A 211 UNP P16304 LEU 211 SEE REMARK 999 SEQADV 3DKV GLN A 217 UNP P16304 LYS 217 SEE REMARK 999 SEQRES 1 A 217 MET ASN ILE VAL LEU MET GLY LEU PRO GLY ALA GLY LYS SEQRES 2 A 217 GLY THR GLN ALA GLU ARG ILE VAL GLU LYS TYR GLY ILE SEQRES 3 A 217 PRO HIS ILE SER THR GLY ASP MET PHE ARG ALA ALA MET SEQRES 4 A 217 LYS GLU GLU THR PRO LEU GLY LEU GLU ALA LYS SER TYR SEQRES 5 A 217 ILE ASP LYS GLY GLU LEU VAL PRO ASP GLU VAL THR ILE SEQRES 6 A 217 GLY ILE VAL ARG GLU ARG LEU SER LYS SER ASP CYS GLU SEQRES 7 A 217 ARG GLY PHE LEU LEU ASP GLY PHE PRO ARG THR VAL ALA SEQRES 8 A 217 GLN ALA GLU ALA LEU GLU GLU ILE LEU GLU GLU MET GLY SEQRES 9 A 217 ARG PRO ILE ASP TYR VAL ILE ASN ILE GLN VAL ASP LYS SEQRES 10 A 217 GLU GLU LEU MET GLU ARG LEU THR GLY ARG ARG ILE CYS SEQRES 11 A 217 SER VAL CYS GLY THR THR TYR HIS LEU VAL PHE ASN PRO SEQRES 12 A 217 PRO LYS THR PRO GLY ILE CYS ASP LYS ASP GLY GLY GLU SEQRES 13 A 217 LEU TYR GLN ARG ALA ASP ASP ASN GLU GLU THR VAL THR SEQRES 14 A 217 LYS ARG LEU GLU VAL ASN MET LYS GLN THR ALA PRO LEU SEQRES 15 A 217 LEU ALA PHE TYR ASP SER LYS GLU VAL LEU VAL ASN VAL SEQRES 16 A 217 ASN GLY GLN GLN ASP ILE GLN ASP VAL PHE ALA ASP VAL SEQRES 17 A 217 LYS VAL ILE LEU GLY GLY LEU LYS GLN HET ZN A 218 1 HET MG A 219 1 HET AP5 A 220 57 HET EDO A 221 4 HET EDO A 222 4 HET EDO A 223 4 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 AP5 C20 H29 N10 O22 P5 FORMUL 5 EDO 3(C2 H6 O2) FORMUL 8 HOH *206(H2 O) HELIX 1 1 GLY A 12 GLY A 25 1 14 HELIX 2 2 THR A 31 GLU A 42 1 12 HELIX 3 3 THR A 43 LYS A 55 1 13 HELIX 4 4 PRO A 60 SER A 73 1 14 HELIX 5 5 LYS A 74 GLY A 80 5 7 HELIX 6 6 THR A 89 GLY A 104 1 16 HELIX 7 7 ASP A 116 GLU A 118 5 3 HELIX 8 8 GLU A 119 GLY A 126 1 8 HELIX 9 9 ARG A 160 ASP A 163 5 4 HELIX 10 10 ASN A 164 LYS A 189 1 26 HELIX 11 11 ASP A 200 GLY A 214 1 15 SHEET 1 A 5 HIS A 28 SER A 30 0 SHEET 2 A 5 PHE A 81 ASP A 84 1 O LEU A 82 N ILE A 29 SHEET 3 A 5 ASN A 2 MET A 6 1 N LEU A 5 O LEU A 83 SHEET 4 A 5 TYR A 109 GLN A 114 1 O ILE A 111 N VAL A 4 SHEET 5 A 5 LEU A 192 ASN A 196 1 O VAL A 195 N GLN A 114 SHEET 1 B 3 THR A 136 HIS A 138 0 SHEET 2 B 3 ARG A 127 CYS A 130 -1 N ARG A 128 O TYR A 137 SHEET 3 B 3 LEU A 157 TYR A 158 -1 O TYR A 158 N ILE A 129 LINK SG CYS A 130 ZN ZN A 218 1555 1555 2.25 LINK SG CYS A 133 ZN ZN A 218 1555 1555 2.32 LINK SG CYS A 150 ZN ZN A 218 1555 1555 2.37 LINK OD2 ASP A 153 ZN ZN A 218 1555 1555 2.14 LINK MG MG A 219 O2B AP5 A 220 1555 1555 2.30 LINK MG MG A 219 O2G AP5 A 220 1555 1555 2.26 LINK MG MG A 219 O1 EDO A 223 1555 1555 2.45 LINK MG MG A 219 O2 EDO A 223 1555 1555 2.57 LINK MG MG A 219 O HOH A 227 1555 1555 2.53 LINK MG MG A 219 O HOH A 238 1555 1555 2.52 CISPEP 1 PHE A 86 PRO A 87 0 -4.20 SITE 1 AC1 4 CYS A 130 CYS A 133 CYS A 150 ASP A 153 SITE 1 AC2 2 HOH A 227 HOH A 238 SITE 1 AC3 39 PRO A 9 GLY A 10 ALA A 11 GLY A 12 SITE 2 AC3 39 LYS A 13 GLY A 14 THR A 15 THR A 31 SITE 3 AC3 39 GLY A 32 ARG A 36 ILE A 53 GLU A 57 SITE 4 AC3 39 THR A 64 GLY A 85 PHE A 86 ARG A 88 SITE 5 AC3 39 GLN A 92 ARG A 123 LEU A 124 ARG A 127 SITE 6 AC3 39 THR A 136 TYR A 137 HIS A 138 PHE A 141 SITE 7 AC3 39 ARG A 160 ARG A 171 GLY A 197 GLN A 199 SITE 8 AC3 39 ILE A 201 HOH A 226 HOH A 228 HOH A 238 SITE 9 AC3 39 HOH A 261 HOH A 272 HOH A 273 HOH A 275 SITE 10 AC3 39 HOH A 293 HOH A 317 HOH A 396 SITE 1 AC4 4 PHE A 141 ASP A 200 ILE A 201 HOH A 353 SITE 1 AC5 6 HIS A 28 ILE A 29 SER A 30 MET A 34 SITE 2 AC5 6 ARG A 71 HOH A 244 SITE 1 AC6 7 GLY A 14 SER A 30 ASP A 33 ARG A 36 SITE 2 AC6 7 ASP A 84 ARG A 160 HOH A 416 CRYST1 44.624 62.056 86.995 90.00 90.00 90.00 P 21 21 21 4 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 0.022409 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016114 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011495 0.00000