HEADER LYASE 13-FEB-19 6QP2 TITLE CRYSTAL STRUCTURE OF THE PLP-BOUND C-S LYASE FROM STAPHYLOCOCCUS TITLE 2 HOMINIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: CONTAINS A LYSINE COVALENTLY ATTACHED TO A PLP COMPND 6 MOLECULE AT POSITION 246. IN ADDITION TO THE PROTEIN SEQUENCE, THIS COMPND 7 ENTITY ALSO CONTAINS ADDITIONAL RESIDUES INTRODUCED BY THE EXPRESSION COMPND 8 VECTOR. (MGGGFA.....ENLYFQGHHHHHHHHHH); COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: POLYHISTIDINE TAG; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: POLYHISTIDINE FROM TAG INTRODUCED BY EXPRESSION VECTOR COMPND 14 BUT FROM UNKNOWN MONOMER. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS HOMINIS; SOURCE 3 ORGANISM_TAXID: 1290; SOURCE 4 GENE: BUZ46_10400; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI MC1061; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1211845; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 9 ORGANISM_TAXID: 32644; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI MC1061; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 1211845 KEYWDS PYRIDOXAL PHOSPHATE BINDING, CYSTEINE-S-CONJUGATE BETA-LYASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR R.HERMAN,M.RUDDEN,A.J.WILKINSON,S.HANAI,G.H.THOMAS REVDAT 3 24-JAN-24 6QP2 1 REMARK REVDAT 2 05-AUG-20 6QP2 1 JRNL REVDAT 1 04-MAR-20 6QP2 0 JRNL AUTH M.RUDDEN,R.HERMAN,M.ROSE,D.BAWDON,D.S.COX,E.DODSON, JRNL AUTH 2 M.T.G.HOLDEN,A.J.WILKINSON,A.G.JAMES,G.H.THOMAS JRNL TITL THE MOLECULAR BASIS OF THIOALCOHOL PRODUCTION IN HUMAN BODY JRNL TITL 2 ODOUR. JRNL REF SCI REP V. 10 12500 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 32719469 JRNL DOI 10.1038/S41598-020-68860-Z REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 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) : 52.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 92869 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4990 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) : 6746 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.3520 REMARK 3 BIN FREE R VALUE SET COUNT : 376 REMARK 3 BIN FREE R VALUE : 0.3760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6337 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 254 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.65000 REMARK 3 B22 (A**2) : 1.13000 REMARK 3 B33 (A**2) : -1.78000 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): 0.099 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.101 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.922 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6611 ; 0.020 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 5878 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8958 ; 1.364 ; 1.651 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13745 ; 0.957 ; 1.640 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 799 ; 7.011 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 351 ;34.935 ;23.789 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1138 ;15.535 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;19.726 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 852 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7377 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1315 ; 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6QP2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1200013299. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97945 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 52.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 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) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 2.62800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 4DQ6 REMARK 200 REMARK 200 REMARK: LONG FLAT YELLOW SHARDS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4% TACSIMATE PH 6.0, 12% PEG 3,350 REMARK 280 (F1: PEG/ION HT), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298.15K 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 27.37550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.04950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.81650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.04950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.37550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.81650 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -5 REMARK 465 GLY A -4 REMARK 465 GLY A -3 REMARK 465 GLY A -2 REMARK 465 PHE A -1 REMARK 465 ALA A 0 REMARK 465 VAL A 1 REMARK 465 ASN A 2 REMARK 465 LYS A 23 REMARK 465 GLY A 24 REMARK 465 TYR A 25 REMARK 465 LEU A 26 REMARK 465 PHE A 27 REMARK 465 GLY A 28 REMARK 465 ASP A 29 REMARK 465 ALA A 30 REMARK 465 ASP A 31 REMARK 465 THR A 32 REMARK 465 SER A 33 REMARK 465 ASP A 34 REMARK 465 LEU A 35 REMARK 465 LYS A 36 REMARK 465 ASP A 37 REMARK 465 ASN A 38 REMARK 465 ASP A 39 REMARK 465 PHE A 403 REMARK 465 GLN A 404 REMARK 465 GLY A 405 REMARK 465 HIS A 406 REMARK 465 HIS A 407 REMARK 465 HIS A 408 REMARK 465 HIS A 409 REMARK 465 HIS A 410 REMARK 465 HIS A 411 REMARK 465 HIS A 412 REMARK 465 HIS A 413 REMARK 465 HIS A 414 REMARK 465 HIS A 415 REMARK 465 MET B -5 REMARK 465 GLY B -4 REMARK 465 GLY B 28 REMARK 465 ASP B 29 REMARK 465 ALA B 30 REMARK 465 ASP B 31 REMARK 465 THR B 32 REMARK 465 SER B 33 REMARK 465 ASP B 34 REMARK 465 LEU B 35 REMARK 465 LYS B 36 REMARK 465 ASP B 37 REMARK 465 ASN B 38 REMARK 465 ASP B 39 REMARK 465 ASN B 400 REMARK 465 LEU B 401 REMARK 465 TYR B 402 REMARK 465 PHE B 403 REMARK 465 GLN B 404 REMARK 465 GLY B 405 REMARK 465 HIS B 406 REMARK 465 HIS B 407 REMARK 465 HIS B 408 REMARK 465 HIS B 409 REMARK 465 HIS B 410 REMARK 465 HIS B 411 REMARK 465 HIS B 412 REMARK 465 HIS B 413 REMARK 465 HIS B 414 REMARK 465 HIS B 415 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 LYS A 246 O - C - N ANGL. DEV. = 11.6 DEGREES REMARK 500 LYS B 246 O - C - N ANGL. DEV. = 13.4 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 44 48.85 -142.31 REMARK 500 MET A 44 54.52 -145.04 REMARK 500 TRP A 45 -91.20 -123.35 REMARK 500 LYS A 68 -18.63 69.28 REMARK 500 LEU A 70 60.89 -115.63 REMARK 500 ASP A 234 55.03 -111.06 REMARK 500 THR A 271 -71.90 -73.07 REMARK 500 THR A 329 170.17 78.20 REMARK 500 VAL A 368 -61.29 79.76 REMARK 500 MET B 44 45.54 -141.77 REMARK 500 TRP B 45 -88.44 -118.93 REMARK 500 LYS B 68 -23.96 76.82 REMARK 500 LEU B 70 57.12 -114.89 REMARK 500 PHE B 274 46.89 -86.12 REMARK 500 THR B 276 90.37 76.40 REMARK 500 THR B 329 168.26 80.19 REMARK 500 VAL B 368 -57.16 76.27 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 383 0.12 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 PLP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6QP1 RELATED DB: PDB REMARK 900 6QP1: SAME PROTEIN BOUND TO L-CYCLOSERINE REMARK 900 RELATED ID: 6QP3 RELATED DB: PDB REMARK 900 6QP3: STRUCTURAL AND FUNCTIONAL HOMOLOGUE FROM B. SUBTILIS REMARK 900 RELATED ID: 6RVI RELATED DB: PDB REMARK 900 6RVI: E362A MUTANT OF THE SAME PROTEIN REMARK 900 RELATED ID: 6RVJ RELATED DB: PDB REMARK 900 6RVJ: G21T G24A MUTANT OF THE SAME PROTEIN DBREF 6QP2 A -5 415 PDB 6QP2 6QP2 -5 415 DBREF 6QP2 B -5 415 PDB 6QP2 6QP2 -5 415 DBREF 6QP2 C -1 4 PDB 6QP2 6QP2 -1 4 SEQRES 1 A 421 MET GLY GLY GLY PHE ALA VAL ASN TYR ASN PHE ASP GLU SEQRES 2 A 421 ILE ILE ASP ARG ARG TYR THR ASN ALA MET ASN VAL GLU SEQRES 3 A 421 GLY TYR LYS GLY TYR LEU PHE GLY ASP ALA ASP THR SER SEQRES 4 A 421 ASP LEU LYS ASP ASN ASP GLU LEU ILE ARG MET TRP VAL SEQRES 5 A 421 ALA ASP MET ASP PHE GLY THR PRO GLU VAL VAL LEU ASN SEQRES 6 A 421 ALA ILE ARG GLU ARG LEU ASN LYS LYS ILE LEU GLY TYR SEQRES 7 A 421 THR ASN VAL PHE GLY SER GLU TYR TYR GLU ALA PHE VAL SEQRES 8 A 421 SER TRP THR LYS LYS ARG TYR GLY PHE THR PHE SER GLN SEQRES 9 A 421 GLU HIS LEU VAL PHE SER HIS GLY ILE VAL ALA GLY LEU SEQRES 10 A 421 ILE GLU LEU VAL GLY TYR ILE CYS ASP LYS ASP ASP LYS SEQRES 11 A 421 ALA LEU ILE VAL THR PRO SER TYR GLY PRO PHE LYS MET SEQRES 12 A 421 ALA CYS ASP LYS ASN HIS ILE SER THR VAL TYR SER PRO SEQRES 13 A 421 LEU ILE ASN HIS HIS GLY TYR TYR GLU ILE ASP PHE ASP SEQRES 14 A 421 ASP VAL ARG LYS LYS VAL GLU THR GLU ASN ILE LYS LEU SEQRES 15 A 421 CYS ILE PHE ALA ASN PRO HIS ASN PRO THR GLY ARG VAL SEQRES 16 A 421 TRP SER GLU GLU GLU LEU ALA THR LEU GLY GLN ILE MET SEQRES 17 A 421 LYS GLU ASN ASP VAL TRP LEU ILE SER ASP GLU ILE HIS SEQRES 18 A 421 CYS ASP ILE LYS ARG SER GLY GLN SER HIS ILE PRO PHE SEQRES 19 A 421 ALA LYS ALA VAL PRO ASP TYR ASP LYS ILE ILE THR THR SEQRES 20 A 421 MET SER GLN SER LYS ALA PHE ASN ILE ALA GLY LEU MET SEQRES 21 A 421 PHE SER ASN ILE ILE ILE GLN ASN GLU SER LEU LEU LYS SEQRES 22 A 421 THR TRP ASN THR HIS HIS PHE GLY THR GLU ASN PRO LEU SEQRES 23 A 421 SER VAL VAL ALA THR GLN ALA ALA TYR GLU LYS GLY GLU SEQRES 24 A 421 GLY TRP LEU GLN ALA MET ASN HIS TYR LEU ASP ASP ASN SEQRES 25 A 421 PHE ASN TYR LEU ALA ASP PHE LEU GLU LYS GLU LEU PRO SEQRES 26 A 421 HIS ALA GLU PHE LYS ILE PRO GLU ALA THR TYR LEU ALA SEQRES 27 A 421 TRP VAL ASP LEU SER TYR TYR ILE LYS GLU LYS ASP ILE SEQRES 28 A 421 ASP GLU SER MET ALA LYS PHE PHE ILE LYS ASN ALA GLY SEQRES 29 A 421 VAL ILE ILE GLU GLY ALA GLU GLN PHE VAL HIS ASN ALA SEQRES 30 A 421 GLU GLY HIS ILE ARG ILE ASN ILE ALA VAL PRO ARG GLU SEQRES 31 A 421 VAL MET LYS LYS GLY LEU GLN LYS ILE LYS ALA ALA LEU SEQRES 32 A 421 VAL GLU ASN LEU TYR PHE GLN GLY HIS HIS HIS HIS HIS SEQRES 33 A 421 HIS HIS HIS HIS HIS SEQRES 1 B 421 MET GLY GLY GLY PHE ALA VAL ASN TYR ASN PHE ASP GLU SEQRES 2 B 421 ILE ILE ASP ARG ARG TYR THR ASN ALA MET ASN VAL GLU SEQRES 3 B 421 GLY TYR LYS GLY TYR LEU PHE GLY ASP ALA ASP THR SER SEQRES 4 B 421 ASP LEU LYS ASP ASN ASP GLU LEU ILE ARG MET TRP VAL SEQRES 5 B 421 ALA ASP MET ASP PHE GLY THR PRO GLU VAL VAL LEU ASN SEQRES 6 B 421 ALA ILE ARG GLU ARG LEU ASN LYS LYS ILE LEU GLY TYR SEQRES 7 B 421 THR ASN VAL PHE GLY SER GLU TYR TYR GLU ALA PHE VAL SEQRES 8 B 421 SER TRP THR LYS LYS ARG TYR GLY PHE THR PHE SER GLN SEQRES 9 B 421 GLU HIS LEU VAL PHE SER HIS GLY ILE VAL ALA GLY LEU SEQRES 10 B 421 ILE GLU LEU VAL GLY TYR ILE CYS ASP LYS ASP ASP LYS SEQRES 11 B 421 ALA LEU ILE VAL THR PRO SER TYR GLY PRO PHE LYS MET SEQRES 12 B 421 ALA CYS ASP LYS ASN HIS ILE SER THR VAL TYR SER PRO SEQRES 13 B 421 LEU ILE ASN HIS HIS GLY TYR TYR GLU ILE ASP PHE ASP SEQRES 14 B 421 ASP VAL ARG LYS LYS VAL GLU THR GLU ASN ILE LYS LEU SEQRES 15 B 421 CYS ILE PHE ALA ASN PRO HIS ASN PRO THR GLY ARG VAL SEQRES 16 B 421 TRP SER GLU GLU GLU LEU ALA THR LEU GLY GLN ILE MET SEQRES 17 B 421 LYS GLU ASN ASP VAL TRP LEU ILE SER ASP GLU ILE HIS SEQRES 18 B 421 CYS ASP ILE LYS ARG SER GLY GLN SER HIS ILE PRO PHE SEQRES 19 B 421 ALA LYS ALA VAL PRO ASP TYR ASP LYS ILE ILE THR THR SEQRES 20 B 421 MET SER GLN SER LYS ALA PHE ASN ILE ALA GLY LEU MET SEQRES 21 B 421 PHE SER ASN ILE ILE ILE GLN ASN GLU SER LEU LEU LYS SEQRES 22 B 421 THR TRP ASN THR HIS HIS PHE GLY THR GLU ASN PRO LEU SEQRES 23 B 421 SER VAL VAL ALA THR GLN ALA ALA TYR GLU LYS GLY GLU SEQRES 24 B 421 GLY TRP LEU GLN ALA MET ASN HIS TYR LEU ASP ASP ASN SEQRES 25 B 421 PHE ASN TYR LEU ALA ASP PHE LEU GLU LYS GLU LEU PRO SEQRES 26 B 421 HIS ALA GLU PHE LYS ILE PRO GLU ALA THR TYR LEU ALA SEQRES 27 B 421 TRP VAL ASP LEU SER TYR TYR ILE LYS GLU LYS ASP ILE SEQRES 28 B 421 ASP GLU SER MET ALA LYS PHE PHE ILE LYS ASN ALA GLY SEQRES 29 B 421 VAL ILE ILE GLU GLY ALA GLU GLN PHE VAL HIS ASN ALA SEQRES 30 B 421 GLU GLY HIS ILE ARG ILE ASN ILE ALA VAL PRO ARG GLU SEQRES 31 B 421 VAL MET LYS LYS GLY LEU GLN LYS ILE LYS ALA ALA LEU SEQRES 32 B 421 VAL GLU ASN LEU TYR PHE GLN GLY HIS HIS HIS HIS HIS SEQRES 33 B 421 HIS HIS HIS HIS HIS SEQRES 1 C 6 HIS HIS HIS HIS HIS HIS HET PLP A 501 15 HET PLP B 501 15 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 4 PLP 2(C8 H10 N O6 P) FORMUL 6 HOH *254(H2 O) HELIX 1 AA1 ALA A 16 GLY A 21 1 6 HELIX 2 AA2 PRO A 54 ASN A 66 1 13 HELIX 3 AA3 SER A 78 GLY A 93 1 16 HELIX 4 AA4 SER A 97 GLU A 99 5 3 HELIX 5 AA5 GLY A 106 CYS A 119 1 14 HELIX 6 AA6 TYR A 132 LYS A 141 1 10 HELIX 7 AA7 ASP A 161 GLU A 172 1 12 HELIX 8 AA8 SER A 191 ASN A 205 1 15 HELIX 9 AA9 PRO A 227 VAL A 232 1 6 HELIX 10 AB1 ILE A 250 MET A 254 5 5 HELIX 11 AB2 ASN A 262 HIS A 273 1 12 HELIX 12 AB3 ASN A 278 GLY A 292 1 15 HELIX 13 AB4 GLY A 292 LEU A 318 1 27 HELIX 14 AB5 LEU A 336 ASP A 344 1 9 HELIX 15 AB6 SER A 348 GLY A 358 1 11 HELIX 16 AB7 GLU A 365 PHE A 367 5 3 HELIX 17 AB8 PRO A 382 GLU A 399 1 18 HELIX 18 AB9 ALA B 16 GLY B 21 1 6 HELIX 19 AC1 GLY B 21 PHE B 27 1 7 HELIX 20 AC2 PRO B 54 ASN B 66 1 13 HELIX 21 AC3 SER B 78 GLY B 93 1 16 HELIX 22 AC4 SER B 97 GLU B 99 5 3 HELIX 23 AC5 GLY B 106 CYS B 119 1 14 HELIX 24 AC6 TYR B 132 LYS B 141 1 10 HELIX 25 AC7 ASP B 161 GLU B 172 1 12 HELIX 26 AC8 SER B 191 ASN B 205 1 15 HELIX 27 AC9 PRO B 227 VAL B 232 1 6 HELIX 28 AD1 ILE B 250 MET B 254 5 5 HELIX 29 AD2 ASN B 262 HIS B 273 1 12 HELIX 30 AD3 ASN B 278 GLY B 292 1 15 HELIX 31 AD4 GLY B 292 LEU B 318 1 27 HELIX 32 AD5 LEU B 336 LYS B 343 1 8 HELIX 33 AD6 SER B 348 GLY B 358 1 11 HELIX 34 AD7 GLU B 365 PHE B 367 5 3 HELIX 35 AD8 PRO B 382 VAL B 398 1 17 SHEET 1 AA1 2 ILE A 42 ARG A 43 0 SHEET 2 AA1 2 VAL A 359 ILE A 360 1 O ILE A 360 N ILE A 42 SHEET 1 AA2 7 LEU A 101 SER A 104 0 SHEET 2 AA2 7 SER A 256 ILE A 260 -1 O ILE A 258 N VAL A 102 SHEET 3 AA2 7 ILE A 238 MET A 242 -1 N MET A 242 O ASN A 257 SHEET 4 AA2 7 TRP A 208 ASP A 212 1 N SER A 211 O ILE A 239 SHEET 5 AA2 7 ILE A 174 ALA A 180 1 N PHE A 179 O ASP A 212 SHEET 6 AA2 7 LYS A 124 THR A 129 1 N LYS A 124 O LYS A 175 SHEET 7 AA2 7 SER A 145 PRO A 150 1 O VAL A 147 N ALA A 125 SHEET 1 AA3 3 LEU A 331 ASP A 335 0 SHEET 2 AA3 3 HIS A 374 ASN A 378 -1 O ILE A 377 N ALA A 332 SHEET 3 AA3 3 GLU A 362 GLY A 363 -1 N GLU A 362 O ARG A 376 SHEET 1 AA4 2 ILE B 42 ARG B 43 0 SHEET 2 AA4 2 VAL B 359 ILE B 360 1 O ILE B 360 N ILE B 42 SHEET 1 AA5 7 LEU B 101 SER B 104 0 SHEET 2 AA5 7 SER B 256 ILE B 259 -1 O ILE B 258 N VAL B 102 SHEET 3 AA5 7 ILE B 238 MET B 242 -1 N THR B 240 O ILE B 259 SHEET 4 AA5 7 TRP B 208 ASP B 212 1 N SER B 211 O ILE B 239 SHEET 5 AA5 7 ILE B 174 ALA B 180 1 N PHE B 179 O ASP B 212 SHEET 6 AA5 7 LYS B 124 THR B 129 1 N LYS B 124 O LYS B 175 SHEET 7 AA5 7 SER B 145 PRO B 150 1 O VAL B 147 N ALA B 125 SHEET 1 AA6 2 ILE B 152 HIS B 154 0 SHEET 2 AA6 2 TYR B 157 GLU B 159 -1 O GLU B 159 N ILE B 152 SHEET 1 AA7 3 LEU B 331 ASP B 335 0 SHEET 2 AA7 3 HIS B 374 ASN B 378 -1 O ILE B 377 N ALA B 332 SHEET 3 AA7 3 GLU B 362 GLY B 363 -1 N GLU B 362 O ARG B 376 LINK NZ LYS A 246 C4A PLP A 501 1555 1555 1.28 LINK NZ LYS B 246 C4A PLP B 501 1555 1555 1.29 CISPEP 1 THR A 129 PRO A 130 0 3.27 CISPEP 2 ASN A 181 PRO A 182 0 7.40 CISPEP 3 ASN A 184 PRO A 185 0 13.76 CISPEP 4 THR B 129 PRO B 130 0 0.23 CISPEP 5 ASN B 181 PRO B 182 0 1.23 CISPEP 6 ASN B 184 PRO B 185 0 15.72 SITE 1 AC1 13 ILE A 107 VAL A 108 TYR A 132 ASN A 184 SITE 2 AC1 13 ASP A 212 ILE A 214 HIS A 215 LYS A 246 SITE 3 AC1 13 HOH A 686 HOH A 699 TYR B 72 HIS C 1 SITE 4 AC1 13 HIS C 2 SITE 1 AC2 12 TYR A 72 GLY B 106 ILE B 107 VAL B 108 SITE 2 AC2 12 TYR B 132 ASN B 184 ASP B 212 ILE B 214 SITE 3 AC2 12 HIS B 215 LYS B 246 HOH B 604 HOH B 629 CRYST1 54.751 113.633 118.099 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 0.018265 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008800 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008467 0.00000