HEADER TRANSFERASE/TRANSFERASE INHIBITOR 08-JAN-15 4XJM TITLE CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BIOA) FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS, COMPLEXED WITH A HTS LEAD COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 7,8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE,DAPA COMPND 5 AMINOTRANSFERASE,8-DIAMINONONANOATE SYNTHASE,DANS,DIAMINOPELARGONIC COMPND 6 ACID SYNTHASE; COMPND 7 EC: 2.6.1.62; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 STRAIN: ATCC 25618 / H37RV; SOURCE 6 GENE: BIOA, RV1568, MTCY336.35C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR COMPLEX TRANSAMINASE PLP, TRANSFERASE-TRANSFERASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.C.FINZEL,R.DAI REVDAT 3 27-SEP-23 4XJM 1 REMARK REVDAT 2 22-JAN-20 4XJM 1 JRNL REMARK LINK SITE REVDAT 2 2 1 ATOM REVDAT 1 20-JAN-16 4XJM 0 JRNL AUTH B.C.FINZEL,R.DAI JRNL TITL FRAGMENT BASED INHIBITOR DESIGN OF MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS BIOA (HTTP://HDL.HANDLE.NET/11299/171084) JRNL REF THESIS, UNIVERSITY OF 2015 JRNL REF 2 MINNESOTA JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 101.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 113212 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5669 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7409 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 392 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6420 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 298 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : -0.43000 REMARK 3 B33 (A**2) : 0.33000 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): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.091 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.578 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6748 ; 0.006 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9251 ; 1.129 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 882 ; 5.338 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 257 ;35.142 ;22.374 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 980 ;12.890 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 50 ;11.394 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1061 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5174 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 : 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4XJM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000205759. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 113212 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 101.945 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.34700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3TFT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 MM HEPES PH 7.5, 50 MM NACL, 0.1 MM REMARK 280 TCEP RESERVOIR:10% PEG 8000, 0.1M MAGNESIUM CHLORIDE, 0.1M HEPES REMARK 280 PH 7.5 CRYO: 15% PEG 400 IN RESERVOIR SOLUTION, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.15K 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 31.52900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.94500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.02600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 101.94500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.52900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.02600 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: 10830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 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 ALA A 3 REMARK 465 ALA A 4 REMARK 465 THR A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 7 REMARK 465 PRO A 437 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 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 ALA B 3 REMARK 465 ALA B 4 REMARK 465 THR B 5 REMARK 465 GLY B 6 REMARK 465 GLY B 7 REMARK 465 PRO B 437 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 ARG A 403 CZ ARG A 403 NH1 -0.930 REMARK 500 ARG A 403 CZ ARG A 403 NH2 0.209 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 A 403 CD - NE - CZ ANGL. DEV. = -16.0 DEGREES REMARK 500 ARG A 403 NH1 - CZ - NH2 ANGL. DEV. = -16.9 DEGREES REMARK 500 ARG A 403 NE - CZ - NH1 ANGL. DEV. = -19.5 DEGREES REMARK 500 ARG A 403 NE - CZ - NH2 ANGL. DEV. = -11.6 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 MET A 87 107.90 -162.40 REMARK 500 MET A 174 67.82 27.20 REMARK 500 THR A 179 -74.25 -43.10 REMARK 500 VAL A 222 -52.00 72.07 REMARK 500 ALA A 373 49.89 -90.39 REMARK 500 ARG A 403 -127.41 49.43 REMARK 500 ARG A 403 -125.24 44.64 REMARK 500 TRP B 65 -0.19 74.99 REMARK 500 MET B 87 107.87 -167.91 REMARK 500 HIS B 89 141.46 -171.78 REMARK 500 MET B 174 74.17 47.25 REMARK 500 ASP B 180 -13.50 85.86 REMARK 500 VAL B 222 -50.36 72.72 REMARK 500 ARG B 403 -117.92 48.44 REMARK 500 SER B 435 -63.77 -95.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 403 0.11 SIDE CHAIN 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 41E A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 41E B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XJL RELATED DB: PDB REMARK 900 RELATED ID: 4XJO RELATED DB: PDB REMARK 900 RELATED ID: 4XJP RELATED DB: PDB DBREF 4XJM A 1 437 UNP P9WQ81 BIOA_MYCTU 1 437 DBREF 4XJM B 1 437 UNP P9WQ81 BIOA_MYCTU 1 437 SEQADV 4XJM MET A -19 UNP P9WQ81 INITIATING METHIONINE SEQADV 4XJM GLY A -18 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM SER A -17 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM SER A -16 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS A -15 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS A -14 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS A -13 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS A -12 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS A -11 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS A -10 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM SER A -9 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM SER A -8 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM GLY A -7 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM LEU A -6 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM VAL A -5 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM PRO A -4 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM ARG A -3 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM GLY A -2 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM SER A -1 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS A 0 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM MET B -19 UNP P9WQ81 INITIATING METHIONINE SEQADV 4XJM GLY B -18 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM SER B -17 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM SER B -16 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS B -15 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS B -14 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS B -13 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS B -12 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS B -11 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS B -10 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM SER B -9 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM SER B -8 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM GLY B -7 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM LEU B -6 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM VAL B -5 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM PRO B -4 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM ARG B -3 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM GLY B -2 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM SER B -1 UNP P9WQ81 EXPRESSION TAG SEQADV 4XJM HIS B 0 UNP P9WQ81 EXPRESSION TAG SEQRES 1 A 457 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 457 LEU VAL PRO ARG GLY SER HIS MET ALA ALA ALA THR GLY SEQRES 3 A 457 GLY LEU THR PRO GLU GLN ILE ILE ALA VAL ASP GLY ALA SEQRES 4 A 457 HIS LEU TRP HIS PRO TYR SER SER ILE GLY ARG GLU ALA SEQRES 5 A 457 VAL SER PRO VAL VAL ALA VAL ALA ALA HIS GLY ALA TRP SEQRES 6 A 457 LEU THR LEU ILE ARG ASP GLY GLN PRO ILE GLU VAL LEU SEQRES 7 A 457 ASP ALA MET SER SER TRP TRP THR ALA ILE HIS GLY HIS SEQRES 8 A 457 GLY HIS PRO ALA LEU ASP GLN ALA LEU THR THR GLN LEU SEQRES 9 A 457 ARG VAL MET ASN HIS VAL MET PHE GLY GLY LEU THR HIS SEQRES 10 A 457 GLU PRO ALA ALA ARG LEU ALA LYS LEU LEU VAL ASP ILE SEQRES 11 A 457 THR PRO ALA GLY LEU ASP THR VAL PHE PHE SER ASP SER SEQRES 12 A 457 GLY SER VAL SER VAL GLU VAL ALA ALA LYS MET ALA LEU SEQRES 13 A 457 GLN TYR TRP ARG GLY ARG GLY LEU PRO GLY LYS ARG ARG SEQRES 14 A 457 LEU MET THR TRP ARG GLY GLY TYR HIS GLY ASP THR PHE SEQRES 15 A 457 LEU ALA MET SER ILE CYS ASP PRO HIS GLY GLY MET HIS SEQRES 16 A 457 SER LEU TRP THR ASP VAL LEU ALA ALA GLN VAL PHE ALA SEQRES 17 A 457 PRO GLN VAL PRO ARG ASP TYR ASP PRO ALA TYR SER ALA SEQRES 18 A 457 ALA PHE GLU ALA GLN LEU ALA GLN HIS ALA GLY GLU LEU SEQRES 19 A 457 ALA ALA VAL VAL VAL GLU PRO VAL VAL GLN GLY ALA GLY SEQRES 20 A 457 GLY MET ARG PHE HIS ASP PRO ARG TYR LEU HIS ASP LEU SEQRES 21 A 457 ARG ASP ILE CYS ARG ARG TYR GLU VAL LEU LEU ILE PHE SEQRES 22 A 457 ASP GLU ILE ALA THR GLY PHE GLY ARG THR GLY ALA LEU SEQRES 23 A 457 PHE ALA ALA ASP HIS ALA GLY VAL SER PRO ASP ILE MET SEQRES 24 A 457 CYS VAL GLY LYS ALA LEU THR GLY GLY TYR LEU SER LEU SEQRES 25 A 457 ALA ALA THR LEU CYS THR ALA ASP VAL ALA HIS THR ILE SEQRES 26 A 457 SER ALA GLY ALA ALA GLY ALA LEU MET HIS GLY PRO THR SEQRES 27 A 457 PHE MET ALA ASN PRO LEU ALA CYS ALA VAL SER VAL ALA SEQRES 28 A 457 SER VAL GLU LEU LEU LEU GLY GLN ASP TRP ARG THR ARG SEQRES 29 A 457 ILE THR GLU LEU ALA ALA GLY LEU THR ALA GLY LEU ASP SEQRES 30 A 457 THR ALA ARG ALA LEU PRO ALA VAL THR ASP VAL ARG VAL SEQRES 31 A 457 CYS GLY ALA ILE GLY VAL ILE GLU CYS ASP ARG PRO VAL SEQRES 32 A 457 ASP LEU ALA VAL ALA THR PRO ALA ALA LEU ASP ARG GLY SEQRES 33 A 457 VAL TRP LEU ARG PRO PHE ARG ASN LEU VAL TYR ALA MET SEQRES 34 A 457 PRO PRO TYR ILE CYS THR PRO ALA GLU ILE THR GLN ILE SEQRES 35 A 457 THR SER ALA MET VAL GLU VAL ALA ARG LEU VAL GLY SER SEQRES 36 A 457 LEU PRO SEQRES 1 B 457 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 457 LEU VAL PRO ARG GLY SER HIS MET ALA ALA ALA THR GLY SEQRES 3 B 457 GLY LEU THR PRO GLU GLN ILE ILE ALA VAL ASP GLY ALA SEQRES 4 B 457 HIS LEU TRP HIS PRO TYR SER SER ILE GLY ARG GLU ALA SEQRES 5 B 457 VAL SER PRO VAL VAL ALA VAL ALA ALA HIS GLY ALA TRP SEQRES 6 B 457 LEU THR LEU ILE ARG ASP GLY GLN PRO ILE GLU VAL LEU SEQRES 7 B 457 ASP ALA MET SER SER TRP TRP THR ALA ILE HIS GLY HIS SEQRES 8 B 457 GLY HIS PRO ALA LEU ASP GLN ALA LEU THR THR GLN LEU SEQRES 9 B 457 ARG VAL MET ASN HIS VAL MET PHE GLY GLY LEU THR HIS SEQRES 10 B 457 GLU PRO ALA ALA ARG LEU ALA LYS LEU LEU VAL ASP ILE SEQRES 11 B 457 THR PRO ALA GLY LEU ASP THR VAL PHE PHE SER ASP SER SEQRES 12 B 457 GLY SER VAL SER VAL GLU VAL ALA ALA LYS MET ALA LEU SEQRES 13 B 457 GLN TYR TRP ARG GLY ARG GLY LEU PRO GLY LYS ARG ARG SEQRES 14 B 457 LEU MET THR TRP ARG GLY GLY TYR HIS GLY ASP THR PHE SEQRES 15 B 457 LEU ALA MET SER ILE CYS ASP PRO HIS GLY GLY MET HIS SEQRES 16 B 457 SER LEU TRP THR ASP VAL LEU ALA ALA GLN VAL PHE ALA SEQRES 17 B 457 PRO GLN VAL PRO ARG ASP TYR ASP PRO ALA TYR SER ALA SEQRES 18 B 457 ALA PHE GLU ALA GLN LEU ALA GLN HIS ALA GLY GLU LEU SEQRES 19 B 457 ALA ALA VAL VAL VAL GLU PRO VAL VAL GLN GLY ALA GLY SEQRES 20 B 457 GLY MET ARG PHE HIS ASP PRO ARG TYR LEU HIS ASP LEU SEQRES 21 B 457 ARG ASP ILE CYS ARG ARG TYR GLU VAL LEU LEU ILE PHE SEQRES 22 B 457 ASP GLU ILE ALA THR GLY PHE GLY ARG THR GLY ALA LEU SEQRES 23 B 457 PHE ALA ALA ASP HIS ALA GLY VAL SER PRO ASP ILE MET SEQRES 24 B 457 CYS VAL GLY LYS ALA LEU THR GLY GLY TYR LEU SER LEU SEQRES 25 B 457 ALA ALA THR LEU CYS THR ALA ASP VAL ALA HIS THR ILE SEQRES 26 B 457 SER ALA GLY ALA ALA GLY ALA LEU MET HIS GLY PRO THR SEQRES 27 B 457 PHE MET ALA ASN PRO LEU ALA CYS ALA VAL SER VAL ALA SEQRES 28 B 457 SER VAL GLU LEU LEU LEU GLY GLN ASP TRP ARG THR ARG SEQRES 29 B 457 ILE THR GLU LEU ALA ALA GLY LEU THR ALA GLY LEU ASP SEQRES 30 B 457 THR ALA ARG ALA LEU PRO ALA VAL THR ASP VAL ARG VAL SEQRES 31 B 457 CYS GLY ALA ILE GLY VAL ILE GLU CYS ASP ARG PRO VAL SEQRES 32 B 457 ASP LEU ALA VAL ALA THR PRO ALA ALA LEU ASP ARG GLY SEQRES 33 B 457 VAL TRP LEU ARG PRO PHE ARG ASN LEU VAL TYR ALA MET SEQRES 34 B 457 PRO PRO TYR ILE CYS THR PRO ALA GLU ILE THR GLN ILE SEQRES 35 B 457 THR SER ALA MET VAL GLU VAL ALA ARG LEU VAL GLY SER SEQRES 36 B 457 LEU PRO HET 41E A 501 29 HET PLP A 502 15 HET 41E B 501 29 HET PLP B 502 15 HETNAM 41E 3-{1-[(5-ACETYLTHIOPHEN-2-YL)CARBONYL]PIPERIDIN-4-YL}- HETNAM 2 41E N-(3-METHOXYPHENYL)PROPANAMIDE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 41E 2(C22 H26 N2 O4 S) FORMUL 4 PLP 2(C8 H10 N O6 P) FORMUL 7 HOH *298(H2 O) HELIX 1 AA1 THR A 9 LEU A 21 1 13 HELIX 2 AA2 MET A 61 THR A 66 1 6 HELIX 3 AA3 HIS A 73 MET A 87 1 15 HELIX 4 AA4 HIS A 97 THR A 111 1 15 HELIX 5 AA5 SER A 123 ARG A 142 1 20 HELIX 6 AA6 THR A 161 SER A 166 1 6 HELIX 7 AA7 ASP A 196 ALA A 211 1 16 HELIX 8 AA8 PRO A 234 GLU A 248 1 15 HELIX 9 AA9 PHE A 267 ALA A 272 5 6 HELIX 10 AB1 ALA A 299 GLY A 308 1 10 HELIX 11 AB2 ASN A 322 GLY A 338 1 17 HELIX 12 AB3 ASP A 340 ASP A 357 1 18 HELIX 13 AB4 THR A 358 LEU A 362 5 5 HELIX 14 AB5 ASP A 384 ASP A 394 1 11 HELIX 15 AB6 THR A 415 GLY A 434 1 20 HELIX 16 AB7 THR B 9 LEU B 21 1 13 HELIX 17 AB8 MET B 61 THR B 66 1 6 HELIX 18 AB9 HIS B 73 ARG B 85 1 13 HELIX 19 AC1 HIS B 97 THR B 111 1 15 HELIX 20 AC2 SER B 123 ARG B 142 1 20 HELIX 21 AC3 THR B 161 SER B 166 1 6 HELIX 22 AC4 ASP B 196 ALA B 211 1 16 HELIX 23 AC5 PRO B 234 GLU B 248 1 15 HELIX 24 AC6 PHE B 267 ALA B 272 5 6 HELIX 25 AC7 ALA B 299 GLY B 308 1 10 HELIX 26 AC8 ASN B 322 GLY B 338 1 17 HELIX 27 AC9 ASP B 340 ASP B 357 1 18 HELIX 28 AD1 THR B 358 LEU B 362 5 5 HELIX 29 AD2 ASP B 384 ASP B 394 1 11 HELIX 30 AD3 THR B 415 GLY B 434 1 20 SHEET 1 AA1 5 VAL A 397 TRP A 398 0 SHEET 2 AA1 5 GLN A 53 ASP A 59 1 N LEU A 58 O TRP A 398 SHEET 3 AA1 5 TRP A 45 ARG A 50 -1 N ARG A 50 O GLN A 53 SHEET 4 AA1 5 VAL A 36 HIS A 42 -1 N VAL A 39 O THR A 47 SHEET 5 AA1 5 LEU B 95 THR B 96 1 O THR B 96 N ALA A 38 SHEET 1 AA2 5 LEU A 95 THR A 96 0 SHEET 2 AA2 5 VAL B 36 HIS B 42 1 O ALA B 38 N THR A 96 SHEET 3 AA2 5 TRP B 45 ARG B 50 -1 O THR B 47 N VAL B 39 SHEET 4 AA2 5 GLN B 53 ASP B 59 -1 O VAL B 57 N LEU B 46 SHEET 5 AA2 5 VAL B 397 TRP B 398 1 O TRP B 398 N LEU B 58 SHEET 1 AA3 7 LEU A 115 SER A 121 0 SHEET 2 AA3 7 ALA A 293 THR A 298 -1 O THR A 295 N PHE A 119 SHEET 3 AA3 7 ILE A 278 VAL A 281 -1 N MET A 279 O LEU A 296 SHEET 4 AA3 7 LEU A 250 ASP A 254 1 N PHE A 253 O CYS A 280 SHEET 5 AA3 7 LEU A 214 VAL A 219 1 N VAL A 217 O ILE A 252 SHEET 6 AA3 7 ARG A 149 TRP A 153 1 N ARG A 149 O ALA A 215 SHEET 7 AA3 7 VAL A 186 ALA A 188 1 O ALA A 188 N THR A 152 SHEET 1 AA4 2 VAL A 223 GLN A 224 0 SHEET 2 AA4 2 ARG A 230 PHE A 231 -1 O ARG A 230 N GLN A 224 SHEET 1 AA5 3 VAL A 365 VAL A 370 0 SHEET 2 AA5 3 GLY A 375 CYS A 379 -1 O GLU A 378 N THR A 366 SHEET 3 AA5 3 LEU A 405 ALA A 408 -1 O VAL A 406 N ILE A 377 SHEET 1 AA6 7 LEU B 115 SER B 121 0 SHEET 2 AA6 7 ALA B 293 THR B 298 -1 O THR B 295 N PHE B 119 SHEET 3 AA6 7 ILE B 278 VAL B 281 -1 N MET B 279 O LEU B 296 SHEET 4 AA6 7 LEU B 250 ASP B 254 1 N PHE B 253 O CYS B 280 SHEET 5 AA6 7 LEU B 214 VAL B 219 1 N VAL B 217 O ILE B 252 SHEET 6 AA6 7 ARG B 149 TRP B 153 1 N ARG B 149 O ALA B 215 SHEET 7 AA6 7 VAL B 186 ALA B 188 1 O ALA B 188 N THR B 152 SHEET 1 AA7 2 VAL B 223 GLN B 224 0 SHEET 2 AA7 2 ARG B 230 PHE B 231 -1 O ARG B 230 N GLN B 224 SHEET 1 AA8 3 VAL B 365 VAL B 370 0 SHEET 2 AA8 3 GLY B 375 CYS B 379 -1 O GLU B 378 N ASP B 367 SHEET 3 AA8 3 LEU B 405 ALA B 408 -1 O VAL B 406 N ILE B 377 LINK NZ LYS A 283 C4A PLP A 502 1555 1555 1.84 LINK NZ LYS B 283 C4A PLP B 502 1555 1555 1.91 SITE 1 AC1 15 TYR A 25 TRP A 64 MET A 165 GLY A 172 SITE 2 AC1 15 GLY A 173 MET A 174 TRP A 178 HOH A 734 SITE 3 AC1 15 MET B 91 GLY B 93 LYS B 133 MET B 314 SITE 4 AC1 15 GLY B 316 PRO B 317 THR B 318 SITE 1 AC2 16 GLY A 124 SER A 125 TYR A 157 HIS A 158 SITE 2 AC2 16 GLY A 159 GLU A 220 ASP A 254 ILE A 256 SITE 3 AC2 16 ALA A 257 LYS A 283 HOH A 621 HOH A 651 SITE 4 AC2 16 HOH A 686 HOH A 725 THR B 318 HOH B 603 SITE 1 AC3 15 MET A 91 GLY A 93 MET A 314 GLY A 316 SITE 2 AC3 15 PRO A 317 THR A 318 PRO B 24 TYR B 25 SITE 3 AC3 15 TRP B 64 MET B 165 GLY B 172 GLY B 173 SITE 4 AC3 15 MET B 174 TRP B 178 PHE B 402 SITE 1 AC4 17 PRO A 317 THR A 318 HOH A 603 GLY B 124 SITE 2 AC4 17 SER B 125 TYR B 157 HIS B 158 GLY B 159 SITE 3 AC4 17 GLU B 220 ASP B 254 ILE B 256 ALA B 257 SITE 4 AC4 17 LYS B 283 HOH B 614 HOH B 645 HOH B 664 SITE 5 AC4 17 HOH B 718 CRYST1 63.058 66.052 203.890 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 0.015858 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004905 0.00000