HEADER LYASE 22-MAR-16 5IW8 TITLE MYCOBACTERIUM TUBERCULOSIS CYSM IN COMPLEX WITH THE UREA-SCAFFOLD TITLE 2 INHIBITOR 4 [5-(3-([1,1'-BIPHENYL]-3-YL)UREIDO)-2-HYDROXYBENZOIC TITLE 3 ACID] COMPND MOL_ID: 1; COMPND 2 MOLECULE: O-PHOSPHOSERINE SULFHYDRYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: OPS SULFHYDRYLASE,CYSO-THIOCARBOXYLATE-DEPENDENT CYSTEINE COMPND 5 SYNTHASE,CYSTEINE SYNTHASE B,CSASE B,O-PHOSPHOSERINE-SPECIFIC COMPND 6 CYSTEINE SYNTHASE,[CYSO SULFUR-CARRIER PROTEIN]-THIOCARBOXYLATE- COMPND 7 DEPENDENT CYSTEINE SYNTHASE; COMPND 8 EC: 2.5.1.113; COMPND 9 ENGINEERED: YES; COMPND 10 MUTATION: YES; COMPND 11 OTHER_DETAILS: T2A MUTATION. LYS51 COVALENT MODIFICATION WITH PLP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 GENE: CYSM, RV1336, MTCY130.21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS MYCOBACTERIUM TUBERCULOSIS, CYSTEINE BIOSYNTHESIS, SULPHUR KEYWDS 2 METABOLISM, INHIBITOR, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR K.BRUNNER,R.SCHNELL,G.SCHNEIDER REVDAT 2 10-JAN-24 5IW8 1 REMARK REVDAT 1 17-AUG-16 5IW8 0 JRNL AUTH K.BRUNNER,S.MARIC,R.S.RESHMA,H.ALMQVIST,B.SEASHORE-LUDLOW, JRNL AUTH 2 A.L.GUSTAVSSON,O.POYRAZ,P.YOGEESWARI,T.LUNDBACK,M.VALLIN, JRNL AUTH 3 D.SRIRAM,R.SCHNELL,G.SCHNEIDER JRNL TITL INHIBITORS OF THE CYSTEINE SYNTHASE CYSM WITH ANTIBACTERIAL JRNL TITL 2 POTENCY AGAINST DORMANT MYCOBACTERIUM TUBERCULOSIS. JRNL REF J.MED.CHEM. V. 59 6848 2016 JRNL REFN ISSN 0022-2623 JRNL PMID 27379713 JRNL DOI 10.1021/ACS.JMEDCHEM.6B00674 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 36652 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1857 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2554 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.3460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4596 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 83 REMARK 3 SOLVENT ATOMS : 446 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.60000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.67000 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): 0.217 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.185 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.139 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.190 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4789 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4542 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6525 ; 1.487 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10389 ; 0.835 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 616 ; 5.904 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;30.615 ;22.857 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 720 ;15.180 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;17.250 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 732 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5516 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1090 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5IW8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-15 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 : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : SI MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38565 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 55.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.900 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.16700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.81900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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: 3DKI REMARK 200 REMARK 200 REMARK: ROD / NEEDLE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES 6 PH 20 %W/V PEG 6K 0.2 M REMARK 280 NH4CL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 33.58200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.39050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.94150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.39050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.58200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.94150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 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 VAL A 227 REMARK 465 PRO A 228 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 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 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 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 GLU A 76 CD OE1 OE2 REMARK 480 GLU B 126 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 O GLN B 111 O HOH B 501 2.01 REMARK 500 O HOH B 621 O HOH B 652 2.16 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 GLU A 76 CG GLU A 76 CD -0.125 REMARK 500 GLU B 126 CB GLU B 126 CG -0.165 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 ARG B 25 NE - CZ - NH1 ANGL. DEV. = 3.6 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 ARG A 25 109.08 -160.58 REMARK 500 PRO A 77 46.86 -94.19 REMARK 500 THR A 186 -1.10 79.06 REMARK 500 SER B 79 -162.13 -118.57 REMARK 500 TYR B 150 77.99 62.30 REMARK 500 THR B 186 -2.72 78.34 REMARK 500 VAL B 216 48.55 36.77 REMARK 500 SER B 302 5.88 -63.14 REMARK 500 ALA B 307 -81.71 -104.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 695 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH A 696 DISTANCE = 6.58 ANGSTROMS REMARK 525 HOH A 697 DISTANCE = 7.08 ANGSTROMS REMARK 525 HOH A 698 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH B 747 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH B 748 DISTANCE = 7.08 ANGSTROMS 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 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 140 O REMARK 620 2 ASN A 143 O 77.9 REMARK 620 3 TRP A 146 O 85.9 84.5 REMARK 620 4 HOH A 603 O 94.2 75.8 159.8 REMARK 620 5 HOH A 654 O 92.6 166.8 85.6 114.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6EC A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6EC B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 402 and LYS B REMARK 800 51 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FGP RELATED DB: PDB REMARK 900 CYSM PROTEIN: LIGAND-FREE STRUCTURE REMARK 900 RELATED ID: 3DKI RELATED DB: PDB REMARK 900 CYSM PROTEIN: LIGAND-FREE STRUCTURE DBREF 5IW8 A 1 323 UNP P9WP53 CYSM_MYCTU 1 323 DBREF 5IW8 B 1 323 UNP P9WP53 CYSM_MYCTU 1 323 SEQADV 5IW8 GLY A -2 UNP P9WP53 EXPRESSION TAG SEQADV 5IW8 SER A -1 UNP P9WP53 EXPRESSION TAG SEQADV 5IW8 HIS A 0 UNP P9WP53 EXPRESSION TAG SEQADV 5IW8 ALA A 2 UNP P9WP53 THR 2 ENGINEERED MUTATION SEQADV 5IW8 GLY B -2 UNP P9WP53 EXPRESSION TAG SEQADV 5IW8 SER B -1 UNP P9WP53 EXPRESSION TAG SEQADV 5IW8 HIS B 0 UNP P9WP53 EXPRESSION TAG SEQADV 5IW8 ALA B 2 UNP P9WP53 THR 2 ENGINEERED MUTATION SEQRES 1 A 326 GLY SER HIS MET ALA ARG TYR ASP SER LEU LEU GLN ALA SEQRES 2 A 326 LEU GLY ASN THR PRO LEU VAL GLY LEU GLN ARG LEU SER SEQRES 3 A 326 PRO ARG TRP ASP ASP GLY ARG ASP GLY PRO HIS VAL ARG SEQRES 4 A 326 LEU TRP ALA LYS LEU GLU ASP ARG ASN PRO THR GLY SER SEQRES 5 A 326 ILE LYS ASP ARG PRO ALA VAL ARG MET ILE GLU GLN ALA SEQRES 6 A 326 GLU ALA ASP GLY LEU LEU ARG PRO GLY ALA THR ILE LEU SEQRES 7 A 326 GLU PRO THR SER GLY ASN THR GLY ILE SER LEU ALA MET SEQRES 8 A 326 ALA ALA ARG LEU LYS GLY TYR ARG LEU ILE CYS VAL MET SEQRES 9 A 326 PRO GLU ASN THR SER VAL GLU ARG ARG GLN LEU LEU GLU SEQRES 10 A 326 LEU TYR GLY ALA GLN ILE ILE PHE SER ALA ALA GLU GLY SEQRES 11 A 326 GLY SER ASN THR ALA VAL ALA THR ALA LYS GLU LEU ALA SEQRES 12 A 326 ALA THR ASN PRO SER TRP VAL MET LEU TYR GLN TYR GLY SEQRES 13 A 326 ASN PRO ALA ASN THR ASP SER HIS TYR CYS GLY THR GLY SEQRES 14 A 326 PRO GLU LEU LEU ALA ASP LEU PRO GLU ILE THR HIS PHE SEQRES 15 A 326 VAL ALA GLY LEU GLY THR THR GLY THR LEU MET GLY THR SEQRES 16 A 326 GLY ARG PHE LEU ARG GLU HIS VAL ALA ASN VAL LYS ILE SEQRES 17 A 326 VAL ALA ALA GLU PRO ARG TYR GLY GLU GLY VAL TYR ALA SEQRES 18 A 326 LEU ARG ASN MET ASP GLU GLY PHE VAL PRO GLU LEU TYR SEQRES 19 A 326 ASP PRO GLU ILE LEU THR ALA ARG TYR SER VAL GLY ALA SEQRES 20 A 326 VAL ASP ALA VAL ARG ARG THR ARG GLU LEU VAL HIS THR SEQRES 21 A 326 GLU GLY ILE PHE ALA GLY ILE SER THR GLY ALA VAL LEU SEQRES 22 A 326 HIS ALA ALA LEU GLY VAL GLY ALA GLY ALA LEU ALA ALA SEQRES 23 A 326 GLY GLU ARG ALA ASP ILE ALA LEU VAL VAL ALA ASP ALA SEQRES 24 A 326 GLY TRP LYS TYR LEU SER THR GLY ALA TYR ALA GLY SER SEQRES 25 A 326 LEU ASP ASP ALA GLU THR ALA LEU GLU GLY GLN LEU TRP SEQRES 26 A 326 ALA SEQRES 1 B 326 GLY SER HIS MET ALA ARG TYR ASP SER LEU LEU GLN ALA SEQRES 2 B 326 LEU GLY ASN THR PRO LEU VAL GLY LEU GLN ARG LEU SER SEQRES 3 B 326 PRO ARG TRP ASP ASP GLY ARG ASP GLY PRO HIS VAL ARG SEQRES 4 B 326 LEU TRP ALA LYS LEU GLU ASP ARG ASN PRO THR GLY SER SEQRES 5 B 326 ILE LYS ASP ARG PRO ALA VAL ARG MET ILE GLU GLN ALA SEQRES 6 B 326 GLU ALA ASP GLY LEU LEU ARG PRO GLY ALA THR ILE LEU SEQRES 7 B 326 GLU PRO THR SER GLY ASN THR GLY ILE SER LEU ALA MET SEQRES 8 B 326 ALA ALA ARG LEU LYS GLY TYR ARG LEU ILE CYS VAL MET SEQRES 9 B 326 PRO GLU ASN THR SER VAL GLU ARG ARG GLN LEU LEU GLU SEQRES 10 B 326 LEU TYR GLY ALA GLN ILE ILE PHE SER ALA ALA GLU GLY SEQRES 11 B 326 GLY SER ASN THR ALA VAL ALA THR ALA LYS GLU LEU ALA SEQRES 12 B 326 ALA THR ASN PRO SER TRP VAL MET LEU TYR GLN TYR GLY SEQRES 13 B 326 ASN PRO ALA ASN THR ASP SER HIS TYR CYS GLY THR GLY SEQRES 14 B 326 PRO GLU LEU LEU ALA ASP LEU PRO GLU ILE THR HIS PHE SEQRES 15 B 326 VAL ALA GLY LEU GLY THR THR GLY THR LEU MET GLY THR SEQRES 16 B 326 GLY ARG PHE LEU ARG GLU HIS VAL ALA ASN VAL LYS ILE SEQRES 17 B 326 VAL ALA ALA GLU PRO ARG TYR GLY GLU GLY VAL TYR ALA SEQRES 18 B 326 LEU ARG ASN MET ASP GLU GLY PHE VAL PRO GLU LEU TYR SEQRES 19 B 326 ASP PRO GLU ILE LEU THR ALA ARG TYR SER VAL GLY ALA SEQRES 20 B 326 VAL ASP ALA VAL ARG ARG THR ARG GLU LEU VAL HIS THR SEQRES 21 B 326 GLU GLY ILE PHE ALA GLY ILE SER THR GLY ALA VAL LEU SEQRES 22 B 326 HIS ALA ALA LEU GLY VAL GLY ALA GLY ALA LEU ALA ALA SEQRES 23 B 326 GLY GLU ARG ALA ASP ILE ALA LEU VAL VAL ALA ASP ALA SEQRES 24 B 326 GLY TRP LYS TYR LEU SER THR GLY ALA TYR ALA GLY SER SEQRES 25 B 326 LEU ASP ASP ALA GLU THR ALA LEU GLU GLY GLN LEU TRP SEQRES 26 B 326 ALA HET 6EC A 401 26 HET NA A 402 1 HET PLP A 403 15 HET 6EC B 401 26 HET PLP B 402 15 HETNAM 6EC 5-{[([1,1'-BIPHENYL]-3-YL)CARBAMOYL]AMINO}-2- HETNAM 2 6EC HYDROXYBENZOIC ACID HETNAM NA SODIUM ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 6EC 2(C20 H16 N2 O4) FORMUL 4 NA NA 1+ FORMUL 5 PLP 2(C8 H10 N O6 P) FORMUL 8 HOH *446(H2 O) HELIX 1 AA1 SER A 6 LEU A 11 5 6 HELIX 2 AA2 ASP A 43 ASN A 45 5 3 HELIX 3 AA3 LYS A 51 ASP A 65 1 15 HELIX 4 AA4 GLY A 80 LYS A 93 1 14 HELIX 5 AA5 SER A 106 TYR A 116 1 11 HELIX 6 AA6 GLY A 127 THR A 142 1 16 HELIX 7 AA7 ASN A 154 GLY A 164 1 11 HELIX 8 AA8 GLY A 164 LEU A 173 1 10 HELIX 9 AA9 THR A 186 VAL A 200 1 15 HELIX 10 AB1 GLY A 243 GLY A 259 1 17 HELIX 11 AB2 GLY A 263 ALA A 283 1 21 HELIX 12 AB3 GLY A 297 GLY A 304 5 8 HELIX 13 AB4 SER A 309 LEU A 317 1 9 HELIX 14 AB5 SER B 6 ALA B 10 5 5 HELIX 15 AB6 LYS B 51 ASP B 65 1 15 HELIX 16 AB7 SER B 79 LYS B 93 1 15 HELIX 17 AB8 SER B 106 ARG B 110 5 5 HELIX 18 AB9 ALA B 124 GLU B 126 5 3 HELIX 19 AC1 GLY B 127 ALA B 141 1 15 HELIX 20 AC2 ASN B 154 GLY B 164 1 11 HELIX 21 AC3 GLY B 164 LEU B 173 1 10 HELIX 22 AC4 THR B 186 VAL B 200 1 15 HELIX 23 AC5 VAL B 216 ARG B 220 5 5 HELIX 24 AC6 GLY B 243 GLY B 259 1 17 HELIX 25 AC7 GLY B 263 GLY B 284 1 22 HELIX 26 AC8 GLY B 297 GLY B 304 5 8 HELIX 27 AC9 SER B 309 LEU B 317 1 9 SHEET 1 AA1 6 LEU A 16 GLY A 18 0 SHEET 2 AA1 6 VAL A 35 LEU A 41 -1 O ALA A 39 N VAL A 17 SHEET 3 AA1 6 ALA A 287 VAL A 293 1 O ALA A 287 N ARG A 36 SHEET 4 AA1 6 HIS A 178 GLY A 182 1 N HIS A 178 O ALA A 290 SHEET 5 AA1 6 LYS A 204 PRO A 210 1 O VAL A 206 N PHE A 179 SHEET 6 AA1 6 ALA A 238 VAL A 242 1 O TYR A 240 N ALA A 207 SHEET 1 AA2 4 GLN A 119 SER A 123 0 SHEET 2 AA2 4 ARG A 96 PRO A 102 1 N CYS A 99 O GLN A 119 SHEET 3 AA2 4 THR A 73 GLU A 76 1 N ILE A 74 O ILE A 98 SHEET 4 AA2 4 TRP A 146 MET A 148 1 O VAL A 147 N LEU A 75 SHEET 1 AA3 6 LEU B 16 GLY B 18 0 SHEET 2 AA3 6 VAL B 35 LEU B 41 -1 O ALA B 39 N VAL B 17 SHEET 3 AA3 6 ALA B 287 VAL B 293 1 O ILE B 289 N ARG B 36 SHEET 4 AA3 6 HIS B 178 GLY B 182 1 N HIS B 178 O ALA B 290 SHEET 5 AA3 6 LYS B 204 PRO B 210 1 O VAL B 206 N PHE B 179 SHEET 6 AA3 6 ALA B 238 VAL B 242 1 O VAL B 242 N GLU B 209 SHEET 1 AA4 4 GLN B 119 SER B 123 0 SHEET 2 AA4 4 ARG B 96 PRO B 102 1 N CYS B 99 O GLN B 119 SHEET 3 AA4 4 THR B 73 GLU B 76 1 N ILE B 74 O ARG B 96 SHEET 4 AA4 4 TRP B 146 MET B 148 1 O VAL B 147 N LEU B 75 LINK NZ LYS A 51 C4A PLP A 403 1555 1555 1.43 LINK NZ LYS B 51 C4A PLP B 402 1555 1555 1.42 LINK O ALA A 140 NA NA A 402 1555 1555 2.37 LINK O ASN A 143 NA NA A 402 1555 1555 2.24 LINK O TRP A 146 NA NA A 402 1555 1555 2.46 LINK NA NA A 402 O HOH A 603 1555 1555 2.41 LINK NA NA A 402 O HOH A 654 1555 1555 2.29 SITE 1 AC1 18 LYS A 51 GLY A 80 ASN A 81 THR A 82 SITE 2 AC1 18 GLN A 151 TYR A 152 GLY A 184 ALA A 208 SITE 3 AC1 18 PRO A 210 VAL A 242 ALA A 247 ILE A 264 SITE 4 AC1 18 SER A 265 ALA A 268 PLP A 403 HOH A 567 SITE 5 AC1 18 HOH A 606 HOH A 637 SITE 1 AC2 5 ALA A 140 ASN A 143 TRP A 146 HOH A 603 SITE 2 AC2 5 HOH A 654 SITE 1 AC3 15 LYS A 51 ASN A 81 GLY A 182 GLY A 184 SITE 2 AC3 15 THR A 185 THR A 186 GLY A 187 THR A 188 SITE 3 AC3 15 SER A 265 ALA A 294 ASP A 295 6EC A 401 SITE 4 AC3 15 HOH A 521 HOH A 556 HOH A 583 SITE 1 AC4 18 LYS B 51 SER B 79 GLY B 80 ASN B 81 SITE 2 AC4 18 THR B 82 ARG B 109 GLN B 151 TYR B 152 SITE 3 AC4 18 GLY B 184 ALA B 208 PRO B 210 LEU B 219 SITE 4 AC4 18 ASN B 221 VAL B 242 ALA B 247 ALA B 268 SITE 5 AC4 18 PLP B 402 HOH B 580 SITE 1 AC5 22 SER B 49 ILE B 50 ASP B 52 ARG B 53 SITE 2 AC5 22 PRO B 54 ALA B 55 ASN B 81 THR B 82 SITE 3 AC5 22 SER B 85 GLY B 182 GLY B 184 THR B 185 SITE 4 AC5 22 THR B 186 GLY B 187 THR B 188 SER B 265 SITE 5 AC5 22 ALA B 294 ASP B 295 6EC B 401 HOH B 551 SITE 6 AC5 22 HOH B 608 HOH B 649 CRYST1 67.164 87.883 100.781 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 0.014889 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009923 0.00000