HEADER TRANSFERASE 22-JUL-08 3DWI TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYSM, THE CYSTEINE TITLE 2 SYNTHASE B CAVEAT 3DWI ABNORMALLY SHORT LINK BETWEEN LYS A51 AND PLP A401 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE SYNTHASE B; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: O-ACETYLSERINE SULFHYDRYLASE B, O-ACETYLSERINE(THIOL)-LYASE COMPND 5 B, CSASE B; COMPND 6 EC: 2.5.1.47; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 ATCC: 25618; SOURCE 6 GENE: CYSM, RV1336, MT1377, MTCY130.21; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS CYSTEINE SYNTHASE, AMINO-ACID BIOSYNTHESIS, CYSTEINE BIOSYNTHESIS, KEYWDS 2 PYRIDOXAL PHOSPHATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.T.JURGENSON,K.E.BURNS,T.P.BEGLEY,S.E.EALICK REVDAT 6 30-AUG-23 3DWI 1 REMARK REVDAT 5 20-OCT-21 3DWI 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 3DWI 1 VERSN REVDAT 3 24-FEB-09 3DWI 1 VERSN REVDAT 2 14-OCT-08 3DWI 1 JRNL REVDAT 1 23-SEP-08 3DWI 0 JRNL AUTH C.T.JURGENSON,K.E.BURNS,T.P.BEGLEY,S.E.EALICK JRNL TITL CRYSTAL STRUCTURE OF A SULFUR CARRIER PROTEIN COMPLEX FOUND JRNL TITL 2 IN THE CYSTEINE BIOSYNTHETIC PATHWAY OF MYCOBACTERIUM JRNL TITL 3 TUBERCULOSIS. JRNL REF BIOCHEMISTRY V. 47 10354 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18771296 JRNL DOI 10.1021/BI800915J REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 15513 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 788 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) : 2.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1010 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4441 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : -0.17000 REMARK 3 B33 (A**2) : 0.24000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.411 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.266 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.190 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.923 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.867 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4569 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6235 ; 2.281 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 601 ; 6.936 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;33.881 ;22.443 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 662 ;20.620 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;19.161 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 717 ; 0.197 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3484 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3092 ; 0.283 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3216 ; 0.341 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 389 ; 0.218 ; 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): 52 ; 0.237 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.291 ; 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): 3031 ; 1.028 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4726 ; 1.512 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1679 ; 2.233 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1509 ; 3.463 ; 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 : 10 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 29 2 REMARK 3 1 B 2 B 29 2 REMARK 3 2 A 32 A 66 2 REMARK 3 2 B 32 B 66 2 REMARK 3 3 A 70 A 124 2 REMARK 3 3 B 70 B 124 2 REMARK 3 4 A 129 A 132 2 REMARK 3 4 B 129 B 132 2 REMARK 3 5 A 138 A 141 2 REMARK 3 5 B 138 B 141 2 REMARK 3 6 A 146 A 201 2 REMARK 3 6 B 146 B 201 2 REMARK 3 7 A 203 A 208 2 REMARK 3 7 B 203 B 208 2 REMARK 3 8 A 227 A 233 2 REMARK 3 8 B 227 B 233 2 REMARK 3 9 A 235 A 284 2 REMARK 3 9 B 235 B 284 2 REMARK 3 10 A 286 A 305 2 REMARK 3 10 B 286 B 305 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1060 ; 0.11 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 893 ; 0.50 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 1060 ; 0.20 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 893 ; 1.01 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3DWI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048576. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.94980 REMARK 200 MONOCHROMATOR : SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15513 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.810 REMARK 200 RESOLUTION RANGE LOW (A) : 48.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24700 REMARK 200 FOR SHELL : 4.100 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 3DWG, CHAIN A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.1, 0.64 M LI2SO4, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 36.18050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.45800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.67550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.45800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.18050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.67550 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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS ONE BIOLOGICAL UNIT WHICH REMARK 300 CONSISTS OF TWO PROTOMERS OF CYSM. 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: 4110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.1 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 ALA A 125 REMARK 465 GLU A 126 REMARK 465 TYR A 212 REMARK 465 GLY A 213 REMARK 465 GLU A 214 REMARK 465 GLY A 215 REMARK 465 VAL A 216 REMARK 465 TYR A 217 REMARK 465 ALA A 218 REMARK 465 LEU A 219 REMARK 465 ARG A 220 REMARK 465 ASN A 221 REMARK 465 MET A 222 REMARK 465 ASP A 223 REMARK 465 GLU A 224 REMARK 465 GLY A 225 REMARK 465 PHE A 226 REMARK 465 THR A 315 REMARK 465 ALA A 316 REMARK 465 LEU A 317 REMARK 465 GLU A 318 REMARK 465 GLY A 319 REMARK 465 GLN A 320 REMARK 465 LEU A 321 REMARK 465 TRP A 322 REMARK 465 ALA A 323 REMARK 465 GLU B 126 REMARK 465 GLY B 127 REMARK 465 GLY B 128 REMARK 465 ALA B 313 REMARK 465 GLU B 314 REMARK 465 THR B 315 REMARK 465 ALA B 316 REMARK 465 LEU B 317 REMARK 465 GLU B 318 REMARK 465 GLY B 319 REMARK 465 GLN B 320 REMARK 465 LEU B 321 REMARK 465 TRP B 322 REMARK 465 ALA B 323 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 MET A 1 CG SD CE REMARK 470 ARG A 30 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 31 CG OD1 OD2 REMARK 470 LEU A 67 CG CD1 CD2 REMARK 470 GLU A 103 CG CD OE1 OE2 REMARK 470 ASN A 104 CG OD1 ND2 REMARK 470 VAL A 107 CG1 CG2 REMARK 470 GLU A 108 CG CD OE1 OE2 REMARK 470 GLN A 111 CG CD OE1 NE2 REMARK 470 SER A 123 OG REMARK 470 VAL A 133 CG1 CG2 REMARK 470 THR A 135 OG1 CG2 REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 GLU A 138 CG CD OE1 OE2 REMARK 470 THR A 142 OG1 CG2 REMARK 470 SER A 145 OG REMARK 470 ASN A 202 CG OD1 ND2 REMARK 470 GLU A 209 CG CD OE1 OE2 REMARK 470 MET B 1 CG SD CE REMARK 470 ARG B 69 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 103 CG CD OE1 OE2 REMARK 470 ASN B 104 CG OD1 ND2 REMARK 470 VAL B 107 CG1 CG2 REMARK 470 GLU B 108 CG CD OE1 OE2 REMARK 470 GLN B 111 CG CD OE1 NE2 REMARK 470 SER B 123 OG REMARK 470 GLU B 138 CG CD OE1 OE2 REMARK 470 GLU B 234 CG CD OE1 OE2 REMARK 470 GLU B 285 CG CD OE1 OE2 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 NZ LYS A 51 C4 PLP A 401 1.80 REMARK 500 CE LYS A 51 C4A PLP A 401 1.86 REMARK 500 O1P PLP A 401 O HOH A 425 1.94 REMARK 500 NZ LYS A 51 O3 PLP A 401 1.95 REMARK 500 N THR B 185 O1P PLP B 401 1.95 REMARK 500 O THR A 131 N THR A 135 2.01 REMARK 500 ND2 ASN B 81 O3 PLP B 401 2.01 REMARK 500 NH2 ARG A 109 O HOH A 465 2.02 REMARK 500 O HOH B 432 O HOH B 480 2.03 REMARK 500 OE1 GLU A 63 O HOH A 424 2.09 REMARK 500 N VAL A 227 O HOH A 461 2.11 REMARK 500 NZ LYS A 51 C3 PLP A 401 2.14 REMARK 500 O HOH B 488 O HOH B 494 2.15 REMARK 500 O HOH A 448 O HOH A 470 2.18 REMARK 500 O HOH B 478 O HOH B 486 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 470 O HOH B 493 4566 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 163 CB CYS A 163 SG -0.102 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 PRO B 54 C - N - CA ANGL. DEV. = -10.3 DEGREES REMARK 500 LEU B 183 CB - CG - CD2 ANGL. DEV. = -11.4 DEGREES REMARK 500 GLY B 308 N - CA - C ANGL. DEV. = 18.2 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 LEU A 19 78.89 -101.53 REMARK 500 ARG A 44 11.00 -68.56 REMARK 500 PRO A 46 -72.70 -28.65 REMARK 500 PRO A 70 127.78 -32.99 REMARK 500 SER A 123 -147.46 -84.01 REMARK 500 TYR A 150 83.30 65.84 REMARK 500 THR A 186 -17.00 101.64 REMARK 500 GLU A 234 23.37 -79.09 REMARK 500 SER A 302 -38.33 -35.77 REMARK 500 ASP A 311 96.50 -62.50 REMARK 500 ALA A 313 52.20 -36.40 REMARK 500 ALA B 10 43.59 -93.07 REMARK 500 ASN B 13 45.40 33.46 REMARK 500 LEU B 19 79.05 -105.27 REMARK 500 ASP B 31 -89.35 -67.00 REMARK 500 ARG B 44 22.74 -78.38 REMARK 500 SER B 123 -124.70 -83.06 REMARK 500 ALA B 124 -108.01 -154.62 REMARK 500 THR B 142 -48.03 -167.40 REMARK 500 TYR B 150 80.16 61.09 REMARK 500 THR B 186 -11.10 98.37 REMARK 500 ASN B 202 -3.18 69.35 REMARK 500 ALA B 218 -36.01 92.67 REMARK 500 GLU B 224 -74.48 -77.53 REMARK 500 SER B 302 -43.49 -25.95 REMARK 500 SER B 309 -22.77 26.43 REMARK 500 ASP B 311 64.00 150.22 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 MET A 1 THR A 2 149.02 REMARK 500 ASP A 312 ALA A 313 139.32 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 SO4 A 324 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 324 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 325 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DWG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYSM-CYSO COMPLEX, REMARK 900 A CYSTEINE SYNTHASE B - ANTIGEN COMPLEX REMARK 900 RELATED ID: 3DWM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS CYSO, AN ANTIGEN REMARK 900 CFP10A DBREF 3DWI A 1 323 UNP P63873 CYSM_MYCTU 1 323 DBREF 3DWI B 1 323 UNP P63873 CYSM_MYCTU 1 323 SEQADV 3DWI ALA A 204 UNP P63873 LYS 204 ENGINEERED MUTATION SEQADV 3DWI ALA B 204 UNP P63873 LYS 204 ENGINEERED MUTATION SEQRES 1 A 323 MET THR ARG TYR ASP SER LEU LEU GLN ALA LEU GLY ASN SEQRES 2 A 323 THR PRO LEU VAL GLY LEU GLN ARG LEU SER PRO ARG TRP SEQRES 3 A 323 ASP ASP GLY ARG ASP GLY PRO HIS VAL ARG LEU TRP ALA SEQRES 4 A 323 LYS LEU GLU ASP ARG ASN PRO THR GLY SER ILE LYS ASP SEQRES 5 A 323 ARG PRO ALA VAL ARG MET ILE GLU GLN ALA GLU ALA ASP SEQRES 6 A 323 GLY LEU LEU ARG PRO GLY ALA THR ILE LEU GLU PRO THR SEQRES 7 A 323 SER GLY ASN THR GLY ILE SER LEU ALA MET ALA ALA ARG SEQRES 8 A 323 LEU LYS GLY TYR ARG LEU ILE CYS VAL MET PRO GLU ASN SEQRES 9 A 323 THR SER VAL GLU ARG ARG GLN LEU LEU GLU LEU TYR GLY SEQRES 10 A 323 ALA GLN ILE ILE PHE SER ALA ALA GLU GLY GLY SER ASN SEQRES 11 A 323 THR ALA VAL ALA THR ALA LYS GLU LEU ALA ALA THR ASN SEQRES 12 A 323 PRO SER TRP VAL MET LEU TYR GLN TYR GLY ASN PRO ALA SEQRES 13 A 323 ASN THR ASP SER HIS TYR CYS GLY THR GLY PRO GLU LEU SEQRES 14 A 323 LEU ALA ASP LEU PRO GLU ILE THR HIS PHE VAL ALA GLY SEQRES 15 A 323 LEU GLY THR THR GLY THR LEU MET GLY THR GLY ARG PHE SEQRES 16 A 323 LEU ARG GLU HIS VAL ALA ASN VAL ALA ILE VAL ALA ALA SEQRES 17 A 323 GLU PRO ARG TYR GLY GLU GLY VAL TYR ALA LEU ARG ASN SEQRES 18 A 323 MET ASP GLU GLY PHE VAL PRO GLU LEU TYR ASP PRO GLU SEQRES 19 A 323 ILE LEU THR ALA ARG TYR SER VAL GLY ALA VAL ASP ALA SEQRES 20 A 323 VAL ARG ARG THR ARG GLU LEU VAL HIS THR GLU GLY ILE SEQRES 21 A 323 PHE ALA GLY ILE SER THR GLY ALA VAL LEU HIS ALA ALA SEQRES 22 A 323 LEU GLY VAL GLY ALA GLY ALA LEU ALA ALA GLY GLU ARG SEQRES 23 A 323 ALA ASP ILE ALA LEU VAL VAL ALA ASP ALA GLY TRP LYS SEQRES 24 A 323 TYR LEU SER THR GLY ALA TYR ALA GLY SER LEU ASP ASP SEQRES 25 A 323 ALA GLU THR ALA LEU GLU GLY GLN LEU TRP ALA SEQRES 1 B 323 MET THR ARG TYR ASP SER LEU LEU GLN ALA LEU GLY ASN SEQRES 2 B 323 THR PRO LEU VAL GLY LEU GLN ARG LEU SER PRO ARG TRP SEQRES 3 B 323 ASP ASP GLY ARG ASP GLY PRO HIS VAL ARG LEU TRP ALA SEQRES 4 B 323 LYS LEU GLU ASP ARG ASN PRO THR GLY SER ILE LYS ASP SEQRES 5 B 323 ARG PRO ALA VAL ARG MET ILE GLU GLN ALA GLU ALA ASP SEQRES 6 B 323 GLY LEU LEU ARG PRO GLY ALA THR ILE LEU GLU PRO THR SEQRES 7 B 323 SER GLY ASN THR GLY ILE SER LEU ALA MET ALA ALA ARG SEQRES 8 B 323 LEU LYS GLY TYR ARG LEU ILE CYS VAL MET PRO GLU ASN SEQRES 9 B 323 THR SER VAL GLU ARG ARG GLN LEU LEU GLU LEU TYR GLY SEQRES 10 B 323 ALA GLN ILE ILE PHE SER ALA ALA GLU GLY GLY SER ASN SEQRES 11 B 323 THR ALA VAL ALA THR ALA LYS GLU LEU ALA ALA THR ASN SEQRES 12 B 323 PRO SER TRP VAL MET LEU TYR GLN TYR GLY ASN PRO ALA SEQRES 13 B 323 ASN THR ASP SER HIS TYR CYS GLY THR GLY PRO GLU LEU SEQRES 14 B 323 LEU ALA ASP LEU PRO GLU ILE THR HIS PHE VAL ALA GLY SEQRES 15 B 323 LEU GLY THR THR GLY THR LEU MET GLY THR GLY ARG PHE SEQRES 16 B 323 LEU ARG GLU HIS VAL ALA ASN VAL ALA ILE VAL ALA ALA SEQRES 17 B 323 GLU PRO ARG TYR GLY GLU GLY VAL TYR ALA LEU ARG ASN SEQRES 18 B 323 MET ASP GLU GLY PHE VAL PRO GLU LEU TYR ASP PRO GLU SEQRES 19 B 323 ILE LEU THR ALA ARG TYR SER VAL GLY ALA VAL ASP ALA SEQRES 20 B 323 VAL ARG ARG THR ARG GLU LEU VAL HIS THR GLU GLY ILE SEQRES 21 B 323 PHE ALA GLY ILE SER THR GLY ALA VAL LEU HIS ALA ALA SEQRES 22 B 323 LEU GLY VAL GLY ALA GLY ALA LEU ALA ALA GLY GLU ARG SEQRES 23 B 323 ALA ASP ILE ALA LEU VAL VAL ALA ASP ALA GLY TRP LYS SEQRES 24 B 323 TYR LEU SER THR GLY ALA TYR ALA GLY SER LEU ASP ASP SEQRES 25 B 323 ALA GLU THR ALA LEU GLU GLY GLN LEU TRP ALA HET SO4 A 324 5 HET PLP A 401 15 HET SO4 B 324 5 HET SO4 B 325 5 HET PLP B 401 15 HETNAM SO4 SULFATE ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 SO4 3(O4 S 2-) FORMUL 4 PLP 2(C8 H10 N O6 P) FORMUL 8 HOH *160(H2 O) HELIX 1 1 SER A 6 LEU A 11 5 6 HELIX 2 2 ASP A 43 ASN A 45 5 3 HELIX 3 3 LYS A 51 ASP A 65 1 15 HELIX 4 4 GLY A 80 LYS A 93 1 14 HELIX 5 5 SER A 106 TYR A 116 1 11 HELIX 6 6 GLY A 128 ASN A 143 1 16 HELIX 7 7 ASN A 154 GLY A 164 1 11 HELIX 8 8 GLY A 164 LEU A 173 1 10 HELIX 9 9 THR A 186 VAL A 200 1 15 HELIX 10 10 GLY A 243 GLY A 259 1 17 HELIX 11 11 GLY A 263 ALA A 283 1 21 HELIX 12 12 GLY A 297 GLY A 304 5 8 HELIX 13 13 SER B 6 ALA B 10 5 5 HELIX 14 14 ASP B 43 ASN B 45 5 3 HELIX 15 15 LYS B 51 ASP B 65 1 15 HELIX 16 16 GLY B 80 LYS B 93 1 14 HELIX 17 17 SER B 106 GLY B 117 1 12 HELIX 18 18 SER B 129 ALA B 141 1 13 HELIX 19 19 ASN B 154 CYS B 163 1 10 HELIX 20 20 GLY B 164 LEU B 173 1 10 HELIX 21 21 THR B 186 VAL B 200 1 15 HELIX 22 22 ASP B 232 LEU B 236 5 5 HELIX 23 23 GLY B 243 GLY B 259 1 17 HELIX 24 24 GLY B 263 GLY B 284 1 22 HELIX 25 25 GLY B 297 GLY B 304 5 8 SHEET 1 A 7 ARG A 3 TYR A 4 0 SHEET 2 A 7 LEU B 16 GLY B 18 1 O LEU B 16 N TYR A 4 SHEET 3 A 7 VAL B 35 LEU B 41 -1 O ALA B 39 N VAL B 17 SHEET 4 A 7 ALA B 287 VAL B 293 1 O ILE B 289 N ARG B 36 SHEET 5 A 7 HIS B 178 GLY B 182 1 N VAL B 180 O ALA B 290 SHEET 6 A 7 ALA B 204 PRO B 210 1 O ALA B 204 N PHE B 179 SHEET 7 A 7 ALA B 238 VAL B 242 1 O TYR B 240 N ALA B 207 SHEET 1 B 7 ALA A 238 SER A 241 0 SHEET 2 B 7 ALA A 204 GLU A 209 1 N ALA A 207 O ALA A 238 SHEET 3 B 7 HIS A 178 GLY A 182 1 N PHE A 179 O VAL A 206 SHEET 4 B 7 ALA A 287 VAL A 293 1 O ALA A 290 N HIS A 178 SHEET 5 B 7 VAL A 35 LEU A 41 1 N ARG A 36 O ILE A 289 SHEET 6 B 7 LEU A 16 GLY A 18 -1 N VAL A 17 O ALA A 39 SHEET 7 B 7 ARG B 3 TYR B 4 1 O TYR B 4 N LEU A 16 SHEET 1 C 4 GLN A 119 SER A 123 0 SHEET 2 C 4 ARG A 96 PRO A 102 1 N CYS A 99 O GLN A 119 SHEET 3 C 4 THR A 73 PRO A 77 1 N ILE A 74 O ARG A 96 SHEET 4 C 4 TRP A 146 MET A 148 1 O VAL A 147 N THR A 73 SHEET 1 D 4 GLN B 119 PHE B 122 0 SHEET 2 D 4 ARG B 96 MET B 101 1 N LEU B 97 O GLN B 119 SHEET 3 D 4 THR B 73 GLU B 76 1 N ILE B 74 O ARG B 96 SHEET 4 D 4 TRP B 146 MET B 148 1 O VAL B 147 N THR B 73 LINK NZ LYS A 51 C4A PLP A 401 1555 1555 1.11 LINK NZ LYS B 51 C4A PLP B 401 1555 1555 1.32 SITE 1 AC1 4 TYR A 240 SER A 241 ASP A 246 HIS A 271 SITE 1 AC2 7 THR B 78 SER B 79 GLY B 80 GLN B 151 SITE 2 AC2 7 TYR B 152 HOH B 494 HOH B 499 SITE 1 AC3 3 ARG B 286 HOH B 481 HOH B 493 SITE 1 AC4 13 LYS A 51 ASN A 81 GLY A 182 LEU A 183 SITE 2 AC4 13 GLY A 184 THR A 185 THR A 186 GLY A 187 SITE 3 AC4 13 THR A 188 SER A 265 ALA A 294 ASP A 295 SITE 4 AC4 13 HOH A 425 SITE 1 AC5 14 LYS B 51 ASN B 81 GLY B 182 GLY B 184 SITE 2 AC5 14 THR B 185 THR B 186 GLY B 187 THR B 188 SITE 3 AC5 14 ALA B 218 LEU B 219 SER B 265 ALA B 294 SITE 4 AC5 14 ASP B 295 HOH B 441 CRYST1 72.361 85.351 98.916 90.00 90.00 90.00 P 21 21 21 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 0.013820 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011716 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010110 0.00000