HEADER LYASE 18-FEB-16 5I7R TITLE MYCOBACTERIUM TUBERCULOSIS CYSM IN COMPLEX WITH THE UREA-SCAFFOLD TITLE 2 INHIBITOR 2 [3-(3-([1,1'-BIPHENYL]-3-YL)UREIDO)BENZOIC ACID] COMPND MOL_ID: 1; COMPND 2 MOLECULE: O-PHOSPHOSERINE SULFHYDRYLASE; COMPND 3 CHAIN: B, A; 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: LYS51 COVALENT MODIFICATION WITH PLP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: CYSM, RV1336, MTCY130.21; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS MYCOBACTERIUM TUBERCULOSIS, CYSTEINE BIOSYNTHESIS, SULPHUR KEYWDS 2 METABOLISM, INHIBITOR, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR R.SCHNELL,S.MARIC,G.SCHNEIDER REVDAT 2 10-JAN-24 5I7R 1 REMARK REVDAT 1 17-AUG-16 5I7R 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. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 62228 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3308 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) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4582 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 217 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4652 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 100 REMARK 3 SOLVENT ATOMS : 209 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.99000 REMARK 3 B22 (A**2) : -1.61000 REMARK 3 B33 (A**2) : -1.38000 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): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.597 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4851 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4596 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6604 ; 1.608 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10513 ; 0.873 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 621 ; 5.825 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;33.092 ;23.150 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 724 ;13.702 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;18.162 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 738 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5593 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1099 ; 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): 2495 ; 2.361 ; 3.142 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2489 ; 2.287 ; 3.140 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3109 ; 3.201 ; 4.699 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3110 ; 3.201 ; 4.699 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2356 ; 3.009 ; 3.478 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2357 ; 3.009 ; 3.479 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3496 ; 4.520 ; 5.087 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5502 ; 5.961 ;25.799 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5503 ; 5.961 ;25.801 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 5I7R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-FEB-16. REMARK 100 THE DEPOSITION ID IS D_1000218434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97242 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65578 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 65.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.71700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 48.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NH4-ACETATE, 0.1M BT PH 5.5, 25% REMARK 280 PEG 3350, 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 36.08500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.79200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.24350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.79200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.08500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.24350 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: 6380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22530 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 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 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ARG A 211 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 ALA A 323 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 3 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG B 3 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 286 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 3 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 25 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 25 NE - CZ - NH2 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 ALA B 10 58.08 -97.28 REMARK 500 TYR B 150 79.11 60.24 REMARK 500 THR B 186 -5.05 83.81 REMARK 500 ASN B 221 69.05 -108.93 REMARK 500 ASN A 104 46.88 -99.70 REMARK 500 TYR A 150 77.36 66.07 REMARK 500 THR A 186 -3.23 80.58 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 PLP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 68W B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 68W A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP A 401 and LYS A REMARK 800 51 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DKI RELATED DB: PDB REMARK 900 CYSM WITHOUT LIGANDS BOUND REMARK 900 RELATED ID: 3FGP RELATED DB: PDB DBREF 5I7R B 1 323 UNP P9WP53 CYSM_MYCTU 1 323 DBREF 5I7R A 1 323 UNP P9WP53 CYSM_MYCTU 1 323 SEQADV 5I7R GLY B -2 UNP P9WP53 EXPRESSION TAG SEQADV 5I7R SER B -1 UNP P9WP53 EXPRESSION TAG SEQADV 5I7R HIS B 0 UNP P9WP53 EXPRESSION TAG SEQADV 5I7R ALA B 2 UNP P9WP53 THR 2 ENGINEERED MUTATION SEQADV 5I7R GLY A -2 UNP P9WP53 EXPRESSION TAG SEQADV 5I7R SER A -1 UNP P9WP53 EXPRESSION TAG SEQADV 5I7R HIS A 0 UNP P9WP53 EXPRESSION TAG SEQADV 5I7R ALA A 2 UNP P9WP53 THR 2 ENGINEERED MUTATION 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 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 HET PLP B 401 15 HET 68W B 402 25 HET ACT B 403 4 HET ACT B 404 4 HET ACT B 405 4 HET PLP A 401 15 HET 68W A 402 25 HET ACT A 403 4 HET ACT A 404 4 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM 68W 3-{[([1,1'-BIPHENYL]-3-YL)CARBAMOYL]AMINO}BENZOIC ACID HETNAM ACT ACETATE ION HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 68W 2(C20 H16 N2 O3) FORMUL 5 ACT 5(C2 H3 O2 1-) FORMUL 12 HOH *209(H2 O) HELIX 1 AA1 SER B 6 ALA B 10 5 5 HELIX 2 AA2 LYS B 51 ASP B 65 1 15 HELIX 3 AA3 GLY B 80 GLY B 94 1 15 HELIX 4 AA4 SER B 106 TYR B 116 1 11 HELIX 5 AA5 ALA B 124 GLU B 126 5 3 HELIX 6 AA6 GLY B 127 THR B 142 1 16 HELIX 7 AA7 ASN B 154 GLY B 164 1 11 HELIX 8 AA8 GLY B 164 LEU B 173 1 10 HELIX 9 AA9 THR B 186 VAL B 200 1 15 HELIX 10 AB1 ASP B 232 LEU B 236 5 5 HELIX 11 AB2 GLY B 243 GLY B 259 1 17 HELIX 12 AB3 GLY B 263 ALA B 283 1 21 HELIX 13 AB4 GLY B 297 GLY B 304 5 8 HELIX 14 AB5 SER B 309 GLU B 314 1 6 HELIX 15 AB6 SER A 6 ALA A 10 5 5 HELIX 16 AB7 LYS A 51 ASP A 65 1 15 HELIX 17 AB8 GLY A 80 GLY A 94 1 15 HELIX 18 AB9 SER A 106 GLY A 117 1 12 HELIX 19 AC1 ALA A 124 GLU A 126 5 3 HELIX 20 AC2 GLY A 127 ASN A 143 1 17 HELIX 21 AC3 ASN A 154 GLY A 164 1 11 HELIX 22 AC4 GLY A 164 LEU A 173 1 10 HELIX 23 AC5 THR A 186 VAL A 200 1 15 HELIX 24 AC6 ASP A 232 LEU A 236 5 5 HELIX 25 AC7 GLY A 243 GLY A 259 1 17 HELIX 26 AC8 GLY A 263 ALA A 283 1 21 HELIX 27 AC9 ALA A 296 GLY A 304 5 9 HELIX 28 AD1 SER A 309 GLU A 318 1 10 SHEET 1 AA1 7 ARG B 3 TYR B 4 0 SHEET 2 AA1 7 LEU A 16 GLY A 18 1 O GLY A 18 N TYR B 4 SHEET 3 AA1 7 VAL A 35 LEU A 41 -1 O ALA A 39 N VAL A 17 SHEET 4 AA1 7 ALA A 287 VAL A 293 1 O ILE A 289 N ARG A 36 SHEET 5 AA1 7 HIS A 178 GLY A 182 1 N VAL A 180 O ALA A 290 SHEET 6 AA1 7 LYS A 204 GLU A 209 1 O VAL A 206 N PHE A 179 SHEET 7 AA1 7 ALA A 238 SER A 241 1 O TYR A 240 N ALA A 207 SHEET 1 AA2 6 LEU B 16 GLY B 18 0 SHEET 2 AA2 6 VAL B 35 LEU B 41 -1 O ALA B 39 N VAL B 17 SHEET 3 AA2 6 ALA B 287 VAL B 293 1 O ILE B 289 N ARG B 36 SHEET 4 AA2 6 HIS B 178 GLY B 182 1 N HIS B 178 O ALA B 290 SHEET 5 AA2 6 LYS B 204 PRO B 210 1 O VAL B 206 N PHE B 179 SHEET 6 AA2 6 ALA B 238 VAL B 242 1 O VAL B 242 N GLU B 209 SHEET 1 AA3 4 GLN B 119 SER B 123 0 SHEET 2 AA3 4 ARG B 96 PRO B 102 1 N CYS B 99 O GLN B 119 SHEET 3 AA3 4 THR B 73 PRO B 77 1 N ILE B 74 O ILE B 98 SHEET 4 AA3 4 TRP B 146 MET B 148 1 O VAL B 147 N LEU B 75 SHEET 1 AA4 4 GLN A 119 SER A 123 0 SHEET 2 AA4 4 ARG A 96 PRO A 102 1 N MET A 101 O ILE A 121 SHEET 3 AA4 4 THR A 73 PRO A 77 1 N ILE A 74 O ARG A 96 SHEET 4 AA4 4 VAL A 147 MET A 148 1 O VAL A 147 N THR A 73 LINK NZ LYS B 51 C4A PLP B 401 1555 1555 1.39 LINK NZ LYS A 51 C4A PLP A 401 1555 1555 1.38 SITE 1 AC1 15 LYS B 51 ASN B 81 GLY B 182 GLY B 184 SITE 2 AC1 15 THR B 185 THR B 186 GLY B 187 THR B 188 SITE 3 AC1 15 SER B 265 ALA B 294 ASP B 295 68W B 402 SITE 4 AC1 15 HOH B 510 HOH B 548 HOH B 564 SITE 1 AC2 19 LYS B 51 GLY B 80 ASN B 81 THR B 82 SITE 2 AC2 19 GLY B 184 ALA B 208 PRO B 210 ALA B 218 SITE 3 AC2 19 ARG B 220 VAL B 242 ALA B 247 ILE B 264 SITE 4 AC2 19 SER B 265 ALA B 268 PLP B 401 HOH B 514 SITE 5 AC2 19 HOH B 538 HOH B 539 HOH B 569 SITE 1 AC3 4 LEU A 7 PRO A 46 ASP B 43 ARG B 44 SITE 1 AC4 5 TRP A 298 ASN B 45 PRO B 46 GLY B 48 SITE 2 AC4 5 HOH B 571 SITE 1 AC5 5 THR B 78 SER B 79 TYR B 152 ASN B 221 SITE 2 AC5 5 HOH B 514 SITE 1 AC6 18 LYS A 51 THR A 78 SER A 79 ASN A 81 SITE 2 AC6 18 THR A 82 GLN A 151 TYR A 152 GLY A 182 SITE 3 AC6 18 GLY A 184 ALA A 208 PRO A 210 VAL A 242 SITE 4 AC6 18 ALA A 247 ILE A 264 SER A 265 ALA A 268 SITE 5 AC6 18 PLP A 401 HOH A 564 SITE 1 AC7 6 ASP A 43 ASN A 45 PRO A 46 GLY A 48 SITE 2 AC7 6 HOH A 524 TRP B 298 SITE 1 AC8 5 LEU A 41 ASP A 43 ARG A 44 LEU B 7 SITE 2 AC8 5 PRO B 46 SITE 1 AC9 22 SER A 49 ILE A 50 ASP A 52 ARG A 53 SITE 2 AC9 22 PRO A 54 ALA A 55 ASN A 81 THR A 82 SITE 3 AC9 22 SER A 85 GLY A 182 GLY A 184 THR A 185 SITE 4 AC9 22 THR A 186 GLY A 187 THR A 188 SER A 265 SITE 5 AC9 22 ALA A 294 ASP A 295 68W A 402 HOH A 519 SITE 6 AC9 22 HOH A 540 HOH A 542 CRYST1 72.170 86.487 101.584 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 0.013856 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009844 0.00000