HEADER OXIDOREDUCTASE 22-SEP-16 5TEM TITLE STRUCTURE OF 4-HYDROXY-TETRAHYDRODIPICOLINATE REDUCTASE FROM VIBRIO TITLE 2 VULNIFICUS WITH 2,6 PYRIDINE DICARBOXYLIC AND NADH COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-HYDROXY-TETRAHYDRODIPICOLINATE REDUCTASE; COMPND 3 CHAIN: C, A; COMPND 4 SYNONYM: HTPA REDUCTASE; COMPND 5 EC: 1.17.1.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 3 ORGANISM_TAXID: 216895; SOURCE 4 STRAIN: CMCP6; SOURCE 5 GENE: DAPB, VV1_0567; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS OXIDOREDUCTASE, LYSINE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR N.MANK,K.ARNETTE,V.KLAPPER,M.CHRUSZCZ REVDAT 3 04-OCT-23 5TEM 1 REMARK REVDAT 2 30-JUN-21 5TEM 1 JRNL REVDAT 1 18-OCT-17 5TEM 0 JRNL AUTH S.POTE,S.KACHHAP,N.J.MANK,L.DANESHIAN,V.KLAPPER,S.PYE, JRNL AUTH 2 A.K.ARNETTE,L.S.SHIMIZU,T.BOROWSKI,M.CHRUSZCZ JRNL TITL COMPARATIVE STRUCTURAL AND MECHANISTIC STUDIES OF JRNL TITL 2 4-HYDROXY-TETRAHYDRODIPICOLINATE REDUCTASES FROM JRNL TITL 3 MYCOBACTERIUM TUBERCULOSIS AND VIBRIO VULNIFICUS. JRNL REF BIOCHIM BIOPHYS ACTA GEN V.1865 29750 2021 JRNL REF 2 SUBJ JRNL REFN ISSN 1872-8006 JRNL PMID 32980502 JRNL DOI 10.1016/J.BBAGEN.2020.129750 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 26798 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1368 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1918 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2720 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3929 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 132 REMARK 3 SOLVENT ATOMS : 245 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.30000 REMARK 3 B22 (A**2) : -1.83000 REMARK 3 B33 (A**2) : 0.53000 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): 0.291 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.204 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4125 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3899 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5606 ; 1.716 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8932 ; 3.831 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 530 ; 5.879 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;35.919 ;24.611 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 647 ;14.357 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;19.388 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 652 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4694 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 908 ; 0.011 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2126 ; 1.477 ; 2.075 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2125 ; 1.476 ; 2.074 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2654 ; 2.448 ; 3.104 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 C 1 266 A 1 266 30406 0.100 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 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 34 REMARK 3 ORIGIN FOR THE GROUP (A): -54.0820 -30.6750 -22.6760 REMARK 3 T TENSOR REMARK 3 T11: 0.2501 T22: 0.0931 REMARK 3 T33: 0.1072 T12: -0.0415 REMARK 3 T13: 0.0155 T23: -0.0357 REMARK 3 L TENSOR REMARK 3 L11: 2.4136 L22: 1.3916 REMARK 3 L33: 3.1396 L12: 1.5636 REMARK 3 L13: -1.1447 L23: -1.5413 REMARK 3 S TENSOR REMARK 3 S11: 0.0336 S12: -0.2106 S13: -0.1396 REMARK 3 S21: -0.0851 S22: 0.0100 S23: -0.1524 REMARK 3 S31: 0.1893 S32: -0.0899 S33: -0.0436 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 35 A 46 REMARK 3 ORIGIN FOR THE GROUP (A): -44.9630 -36.0030 -31.8470 REMARK 3 T TENSOR REMARK 3 T11: 0.1736 T22: 0.2686 REMARK 3 T33: 0.5809 T12: -0.1857 REMARK 3 T13: -0.0312 T23: 0.1335 REMARK 3 L TENSOR REMARK 3 L11: 4.7946 L22: 9.1439 REMARK 3 L33: 3.5107 L12: -5.7252 REMARK 3 L13: -3.8675 L23: 3.6775 REMARK 3 S TENSOR REMARK 3 S11: -0.0036 S12: 0.2608 S13: -0.6292 REMARK 3 S21: 0.2815 S22: -0.8910 S23: -0.2493 REMARK 3 S31: -0.1410 S32: 0.0527 S33: 0.8945 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 47 A 56 REMARK 3 ORIGIN FOR THE GROUP (A): -47.8990 -37.4630 -20.2890 REMARK 3 T TENSOR REMARK 3 T11: 0.1133 T22: 0.0669 REMARK 3 T33: 0.0970 T12: -0.0418 REMARK 3 T13: 0.0038 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 12.8371 L22: 1.6676 REMARK 3 L33: 7.5706 L12: 2.7069 REMARK 3 L13: 3.4617 L23: -1.9669 REMARK 3 S TENSOR REMARK 3 S11: -0.0388 S12: 0.5569 S13: -0.1737 REMARK 3 S21: -0.0375 S22: 0.0539 S23: -0.0561 REMARK 3 S31: 0.0783 S32: 0.2944 S33: -0.0152 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 57 A 111 REMARK 3 ORIGIN FOR THE GROUP (A): -58.7320 -26.5690 -35.5900 REMARK 3 T TENSOR REMARK 3 T11: 0.2534 T22: 0.0350 REMARK 3 T33: 0.0297 T12: -0.0542 REMARK 3 T13: 0.0169 T23: -0.0207 REMARK 3 L TENSOR REMARK 3 L11: 0.3804 L22: 1.5798 REMARK 3 L33: 2.2858 L12: 0.4753 REMARK 3 L13: 0.1694 L23: -1.2623 REMARK 3 S TENSOR REMARK 3 S11: -0.1240 S12: 0.0636 S13: -0.0981 REMARK 3 S21: -0.2285 S22: 0.1713 S23: -0.1234 REMARK 3 S31: 0.0543 S32: -0.1007 S33: -0.0473 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 112 A 266 REMARK 3 ORIGIN FOR THE GROUP (A): -54.0530 -6.1860 -26.5260 REMARK 3 T TENSOR REMARK 3 T11: 0.2324 T22: 0.0742 REMARK 3 T33: 0.0092 T12: 0.0022 REMARK 3 T13: -0.0027 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.2991 L22: 0.7894 REMARK 3 L33: 0.1931 L12: 0.4781 REMARK 3 L13: 0.0734 L23: 0.0748 REMARK 3 S TENSOR REMARK 3 S11: -0.0395 S12: 0.0200 S13: -0.0076 REMARK 3 S21: -0.0403 S22: 0.0270 S23: -0.0176 REMARK 3 S31: -0.0328 S32: -0.0713 S33: 0.0124 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 : C 1 C 34 REMARK 3 ORIGIN FOR THE GROUP (A): -29.2510 -31.7120 -8.6190 REMARK 3 T TENSOR REMARK 3 T11: 0.2383 T22: 0.0329 REMARK 3 T33: 0.0652 T12: 0.0362 REMARK 3 T13: -0.0006 T23: 0.0308 REMARK 3 L TENSOR REMARK 3 L11: 3.0451 L22: 2.0439 REMARK 3 L33: 2.1814 L12: -0.6439 REMARK 3 L13: -1.2348 L23: 2.0421 REMARK 3 S TENSOR REMARK 3 S11: 0.0215 S12: 0.1533 S13: -0.0087 REMARK 3 S21: 0.0014 S22: 0.0411 S23: -0.0408 REMARK 3 S31: 0.0379 S32: -0.0005 S33: -0.0626 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 : C 35 C 56 REMARK 3 ORIGIN FOR THE GROUP (A): -37.8210 -37.0640 -4.5060 REMARK 3 T TENSOR REMARK 3 T11: 0.0529 T22: 0.0714 REMARK 3 T33: 0.1748 T12: -0.0030 REMARK 3 T13: -0.0236 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 1.1110 L22: 2.0011 REMARK 3 L33: 7.7376 L12: 1.3715 REMARK 3 L13: 1.0150 L23: 0.6120 REMARK 3 S TENSOR REMARK 3 S11: 0.0252 S12: -0.0314 S13: -0.1007 REMARK 3 S21: -0.0415 S22: -0.0012 S23: 0.0656 REMARK 3 S31: 0.2874 S32: -0.4089 S33: -0.0240 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 : C 57 C 127 REMARK 3 ORIGIN FOR THE GROUP (A): -23.4470 -26.1360 3.6340 REMARK 3 T TENSOR REMARK 3 T11: 0.2099 T22: 0.0501 REMARK 3 T33: 0.0085 T12: 0.0459 REMARK 3 T13: -0.0041 T23: 0.0069 REMARK 3 L TENSOR REMARK 3 L11: 0.6501 L22: 0.9599 REMARK 3 L33: 1.6881 L12: -0.0452 REMARK 3 L13: 0.0961 L23: -0.1801 REMARK 3 S TENSOR REMARK 3 S11: -0.0442 S12: -0.0168 S13: 0.0013 REMARK 3 S21: 0.1233 S22: 0.1312 S23: 0.0455 REMARK 3 S31: -0.0129 S32: 0.0731 S33: -0.0869 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 : C 128 C 239 REMARK 3 ORIGIN FOR THE GROUP (A): -30.7400 -1.7470 -4.7010 REMARK 3 T TENSOR REMARK 3 T11: 0.2534 T22: 0.0576 REMARK 3 T33: 0.0226 T12: 0.0075 REMARK 3 T13: -0.0145 T23: 0.0188 REMARK 3 L TENSOR REMARK 3 L11: 0.3627 L22: 1.0059 REMARK 3 L33: 0.0509 L12: -0.1097 REMARK 3 L13: 0.0447 L23: -0.1441 REMARK 3 S TENSOR REMARK 3 S11: 0.0037 S12: -0.0692 S13: -0.0324 REMARK 3 S21: 0.0149 S22: -0.0220 S23: -0.0127 REMARK 3 S31: 0.0133 S32: 0.0247 S33: 0.0182 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 : C 240 C 266 REMARK 3 ORIGIN FOR THE GROUP (A): -17.2050 -21.9840 -7.7690 REMARK 3 T TENSOR REMARK 3 T11: 0.1463 T22: 0.1369 REMARK 3 T33: 0.0173 T12: -0.0029 REMARK 3 T13: 0.0430 T23: -0.0160 REMARK 3 L TENSOR REMARK 3 L11: 1.3330 L22: 4.1850 REMARK 3 L33: 4.0201 L12: 0.6942 REMARK 3 L13: 2.3073 L23: 1.4937 REMARK 3 S TENSOR REMARK 3 S11: -0.1678 S12: 0.2477 S13: -0.0963 REMARK 3 S21: -0.3663 S22: 0.3337 S23: -0.0760 REMARK 3 S31: -0.3063 S32: 0.4530 S33: -0.1659 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 : 1.20 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 5TEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 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-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28190 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 65.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : 0.11200 REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: 1ARZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M BIS-TRIS PH 6.5, 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 40.31950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.29400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.31950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.29400 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 19240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -125.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -80.63900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ASN C 267 REMARK 465 ASP C 268 REMARK 465 LEU C 269 REMARK 465 ASN A 267 REMARK 465 ASP A 268 REMARK 465 LEU A 269 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU C 37 CG CD OE1 OE2 REMARK 470 LYS C 53 CG CD CE NZ REMARK 470 LYS C 199 CG CD CE NZ REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 LYS A 53 CG CD CE NZ REMARK 470 LYS A 138 CD CE NZ REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 LYS A 199 CG CD CE NZ 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 ARG A 107 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 190 NE - CZ - NH1 ANGL. DEV. = -3.5 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 ASP C 61 118.13 -161.15 REMARK 500 THR C 76 -101.56 -131.35 REMARK 500 HIS C 156 154.10 -48.03 REMARK 500 GLU C 252 -2.06 66.00 REMARK 500 ASP A 61 117.39 -160.94 REMARK 500 THR A 76 -104.66 -134.02 REMARK 500 HIS A 156 152.86 -46.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD C 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PDC C 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PDC A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1005 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TEK RELATED DB: PDB REMARK 900 RELATED ID: 5TEN RELATED DB: PDB DBREF 5TEM C 1 269 UNP Q8DEM0 DAPB_VIBVU 1 269 DBREF 5TEM A 1 269 UNP Q8DEM0 DAPB_VIBVU 1 269 SEQRES 1 C 269 MET VAL ARG ILE ALA VAL ALA GLY ALA ALA GLY ARG MET SEQRES 2 C 269 GLY ARG ASN LEU VAL LYS ALA ALA HIS HIS ASN PRO VAL SEQRES 3 C 269 ALA LYS VAL ALA ALA GLY SER GLU ARG PRO GLU SER SER SEQRES 4 C 269 LEU VAL GLY VAL ASP LEU GLY GLU LEU CYS GLY GLU GLY SEQRES 5 C 269 LYS PHE ASP VAL VAL VAL CYS ASP ASP LEU ALA LYS GLN SEQRES 6 C 269 ILE ASP GLN PHE ASP VAL ILE ILE ASP PHE THR ALA PRO SEQRES 7 C 269 ALA SER THR LEU ASN ASN LEU ALA LEU CYS GLN GLN TYR SEQRES 8 C 269 GLY LYS SER ILE VAL ILE GLY THR THR GLY PHE THR GLU SEQRES 9 C 269 GLU GLN ARG GLU GLN ILE ASP LEU VAL ALA GLN GLN VAL SEQRES 10 C 269 PRO VAL VAL MET ALA PRO ASN TYR SER VAL GLY VAL ASN SEQRES 11 C 269 LEU VAL PHE LYS LEU LEU GLU LYS ALA ALA LYS VAL MET SEQRES 12 C 269 GLY ASP TYR CYS ASP ILE GLU ILE VAL GLU ALA HIS HIS SEQRES 13 C 269 ARG HIS LYS VAL ASP ALA PRO SER GLY THR ALA ILE GLY SEQRES 14 C 269 MET GLY GLU ALA ILE ALA GLY ALA MET GLY ASN LYS LEU SEQRES 15 C 269 SER ASP VAL ALA VAL TYR ALA ARG GLU GLY ILE THR GLY SEQRES 16 C 269 GLU ARG THR LYS ASP GLU ILE GLY PHE ALA THR ILE ARG SEQRES 17 C 269 ALA GLY ASP ILE VAL GLY GLU HIS THR ALA MET PHE ALA SEQRES 18 C 269 ASP ILE GLY GLU ARG VAL GLU ILE THR HIS LYS ALA THR SEQRES 19 C 269 ASP ARG MET THR PHE ALA ASN GLY ALA VAL LYS ALA ALA SEQRES 20 C 269 VAL TRP LEU HIS GLU LYS PRO ALA GLY PHE TYR THR MET SEQRES 21 C 269 THR ASP VAL LEU GLY LEU ASN ASP LEU SEQRES 1 A 269 MET VAL ARG ILE ALA VAL ALA GLY ALA ALA GLY ARG MET SEQRES 2 A 269 GLY ARG ASN LEU VAL LYS ALA ALA HIS HIS ASN PRO VAL SEQRES 3 A 269 ALA LYS VAL ALA ALA GLY SER GLU ARG PRO GLU SER SER SEQRES 4 A 269 LEU VAL GLY VAL ASP LEU GLY GLU LEU CYS GLY GLU GLY SEQRES 5 A 269 LYS PHE ASP VAL VAL VAL CYS ASP ASP LEU ALA LYS GLN SEQRES 6 A 269 ILE ASP GLN PHE ASP VAL ILE ILE ASP PHE THR ALA PRO SEQRES 7 A 269 ALA SER THR LEU ASN ASN LEU ALA LEU CYS GLN GLN TYR SEQRES 8 A 269 GLY LYS SER ILE VAL ILE GLY THR THR GLY PHE THR GLU SEQRES 9 A 269 GLU GLN ARG GLU GLN ILE ASP LEU VAL ALA GLN GLN VAL SEQRES 10 A 269 PRO VAL VAL MET ALA PRO ASN TYR SER VAL GLY VAL ASN SEQRES 11 A 269 LEU VAL PHE LYS LEU LEU GLU LYS ALA ALA LYS VAL MET SEQRES 12 A 269 GLY ASP TYR CYS ASP ILE GLU ILE VAL GLU ALA HIS HIS SEQRES 13 A 269 ARG HIS LYS VAL ASP ALA PRO SER GLY THR ALA ILE GLY SEQRES 14 A 269 MET GLY GLU ALA ILE ALA GLY ALA MET GLY ASN LYS LEU SEQRES 15 A 269 SER ASP VAL ALA VAL TYR ALA ARG GLU GLY ILE THR GLY SEQRES 16 A 269 GLU ARG THR LYS ASP GLU ILE GLY PHE ALA THR ILE ARG SEQRES 17 A 269 ALA GLY ASP ILE VAL GLY GLU HIS THR ALA MET PHE ALA SEQRES 18 A 269 ASP ILE GLY GLU ARG VAL GLU ILE THR HIS LYS ALA THR SEQRES 19 A 269 ASP ARG MET THR PHE ALA ASN GLY ALA VAL LYS ALA ALA SEQRES 20 A 269 VAL TRP LEU HIS GLU LYS PRO ALA GLY PHE TYR THR MET SEQRES 21 A 269 THR ASP VAL LEU GLY LEU ASN ASP LEU HET NAD C1001 44 HET PDC C1002 12 HET SO4 C1003 5 HET NAD A1001 44 HET PDC A1002 12 HET SO4 A1003 5 HET SO4 A1004 5 HET SO4 A1005 5 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM PDC PYRIDINE-2,6-DICARBOXYLIC ACID HETNAM SO4 SULFATE ION HETSYN PDC DIPICOLINIC ACID FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 PDC 2(C7 H5 N O4) FORMUL 5 SO4 4(O4 S 2-) FORMUL 11 HOH *245(H2 O) HELIX 1 AA1 GLY C 11 ASN C 24 1 14 HELIX 2 AA2 LEU C 45 CYS C 49 5 5 HELIX 3 AA3 ASP C 61 PHE C 69 5 9 HELIX 4 AA4 ALA C 77 GLY C 92 1 16 HELIX 5 AA5 THR C 103 ALA C 114 1 12 HELIX 6 AA6 SER C 126 GLY C 144 1 19 HELIX 7 AA7 SER C 164 MET C 178 1 15 HELIX 8 AA8 LYS C 181 VAL C 185 1 5 HELIX 9 AA9 ARG C 236 HIS C 251 1 16 HELIX 10 AB1 THR C 259 GLY C 265 1 7 HELIX 11 AB2 GLY A 11 ASN A 24 1 14 HELIX 12 AB3 ASP A 61 PHE A 69 5 9 HELIX 13 AB4 ALA A 77 GLY A 92 1 16 HELIX 14 AB5 THR A 103 ALA A 114 1 12 HELIX 15 AB6 SER A 126 GLY A 144 1 19 HELIX 16 AB7 ASP A 145 CYS A 147 5 3 HELIX 17 AB8 SER A 164 MET A 178 1 15 HELIX 18 AB9 LYS A 181 VAL A 185 1 5 HELIX 19 AC1 ARG A 236 HIS A 251 1 16 HELIX 20 AC2 THR A 259 GLY A 265 1 7 SHEET 1 AA1 7 VAL C 58 CYS C 59 0 SHEET 2 AA1 7 ALA C 27 SER C 33 1 N GLY C 32 O CYS C 59 SHEET 3 AA1 7 VAL C 2 ALA C 7 1 N ILE C 4 O LYS C 28 SHEET 4 AA1 7 VAL C 71 ASP C 74 1 O VAL C 71 N ALA C 5 SHEET 5 AA1 7 SER C 94 ILE C 97 1 O VAL C 96 N ASP C 74 SHEET 6 AA1 7 PRO C 118 MET C 121 1 O VAL C 120 N ILE C 97 SHEET 7 AA1 7 GLY C 256 TYR C 258 1 O TYR C 258 N VAL C 119 SHEET 1 AA2 5 ALA C 186 VAL C 187 0 SHEET 2 AA2 5 ILE C 202 ARG C 208 1 O ILE C 202 N VAL C 187 SHEET 3 AA2 5 ASP C 148 HIS C 155 1 N ILE C 151 O GLY C 203 SHEET 4 AA2 5 GLY C 214 ALA C 221 -1 O ALA C 221 N ASP C 148 SHEET 5 AA2 5 ARG C 226 ALA C 233 -1 O ALA C 233 N GLY C 214 SHEET 1 AA3 7 VAL A 58 CYS A 59 0 SHEET 2 AA3 7 ALA A 27 SER A 33 1 N GLY A 32 O CYS A 59 SHEET 3 AA3 7 VAL A 2 ALA A 7 1 N ILE A 4 O LYS A 28 SHEET 4 AA3 7 VAL A 71 ASP A 74 1 O VAL A 71 N ALA A 5 SHEET 5 AA3 7 SER A 94 ILE A 97 1 O VAL A 96 N ASP A 74 SHEET 6 AA3 7 PRO A 118 MET A 121 1 O VAL A 120 N ILE A 97 SHEET 7 AA3 7 GLY A 256 TYR A 258 1 O TYR A 258 N VAL A 119 SHEET 1 AA4 5 ALA A 186 VAL A 187 0 SHEET 2 AA4 5 ILE A 202 ARG A 208 1 O ILE A 202 N VAL A 187 SHEET 3 AA4 5 ASP A 148 HIS A 155 1 N ILE A 151 O GLY A 203 SHEET 4 AA4 5 GLY A 214 ALA A 221 -1 O ALA A 221 N ASP A 148 SHEET 5 AA4 5 ARG A 226 ALA A 233 -1 O ALA A 233 N GLY A 214 CISPEP 1 ALA C 162 PRO C 163 0 -11.96 CISPEP 2 ALA A 162 PRO A 163 0 -8.78 SITE 1 AC1 25 GLY C 8 GLY C 11 ARG C 12 MET C 13 SITE 2 AC1 25 SER C 33 GLU C 34 ARG C 35 PHE C 75 SITE 3 AC1 25 THR C 76 SER C 80 GLY C 98 THR C 100 SITE 4 AC1 25 ALA C 122 PRO C 123 ASN C 124 TYR C 125 SITE 5 AC1 25 LYS C 159 PDC C1002 HOH C1112 HOH C1126 SITE 6 AC1 25 HOH C1128 HOH C1145 HOH C1157 HOH C1160 SITE 7 AC1 25 HOH C1181 SITE 1 AC2 12 THR C 100 PRO C 123 HIS C 156 LYS C 159 SITE 2 AC2 12 SER C 164 GLY C 165 THR C 166 NAD C1001 SITE 3 AC2 12 HOH C1112 HOH C1129 HOH C1145 HOH C1156 SITE 1 AC3 4 GLN A 89 LYS C 19 HIS C 23 MET C 237 SITE 1 AC4 25 GLY A 8 GLY A 11 ARG A 12 MET A 13 SITE 2 AC4 25 SER A 33 GLU A 34 ARG A 35 PHE A 75 SITE 3 AC4 25 THR A 76 SER A 80 GLY A 98 THR A 100 SITE 4 AC4 25 ALA A 122 PRO A 123 ASN A 124 TYR A 125 SITE 5 AC4 25 LYS A 159 PHE A 239 PDC A1002 HOH A1116 SITE 6 AC4 25 HOH A1122 HOH A1130 HOH A1148 HOH A1154 SITE 7 AC4 25 HOH A1165 SITE 1 AC5 11 THR A 100 PRO A 123 HIS A 156 LYS A 159 SITE 2 AC5 11 SER A 164 GLY A 165 THR A 166 NAD A1001 SITE 3 AC5 11 HOH A1123 HOH A1130 HOH A1165 SITE 1 AC6 4 GLU A 37 SER A 38 SER A 39 HOH A1182 SITE 1 AC7 3 ARG A 157 HIS A 158 ILE A 223 SITE 1 AC8 3 THR A 103 GLU A 104 HOH A1187 CRYST1 80.639 112.588 62.432 90.00 90.00 90.00 P 21 21 2 8 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 0.012401 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016017 0.00000