HEADER TRANSFERASE 26-SEP-07 2Z9U TITLE CRYSTAL STRUCTURE OF PYRIDOXAMINE-PYRUVATE AMINOTRANSFERASE FROM TITLE 2 MESORHIZOBIUM LOTI AT 2.0 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASPARTATE AMINOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PYRIDOXAMINE-PYRUVATE AMINOTRANSFERASE; COMPND 5 EC: 2.6.1.30; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESORHIZOBIUM LOTI; SOURCE 3 ORGANISM_TAXID: 381; SOURCE 4 STRAIN: MAFF303099; SOURCE 5 GENE: MLR6806; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS AMINOTRANSFERASE, PYRIDOXAMINE, PYRUVATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.YOSHIKANE,N.YOKOCHI,M.YAMASAKI,K.MIZUTANI,K.OHNISHI,B.MIKAMI, AUTHOR 2 H.HAYASHI,T.YAGI REVDAT 5 01-NOV-23 2Z9U 1 REMARK REVDAT 4 13-JUL-11 2Z9U 1 VERSN REVDAT 3 24-FEB-09 2Z9U 1 VERSN REVDAT 2 03-JUN-08 2Z9U 1 JRNL REVDAT 1 06-NOV-07 2Z9U 0 JRNL AUTH Y.YOSHIKANE,N.YOKOCHI,M.YAMASAKI,K.MIZUTANI,K.OHNISHI, JRNL AUTH 2 B.MIKAMI,H.HAYASHI,T.YAGI JRNL TITL CRYSTAL STRUCTURE OF PYRIDOXAMINE-PYRUVATE AMINOTRANSFERASE JRNL TITL 2 FROM MESORHIZOBIUM LOTI MAFF303099 JRNL REF J.BIOL.CHEM. V. 283 1120 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 17989071 JRNL DOI 10.1074/JBC.M708061200 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 47892 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2551 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3441 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.1800 REMARK 3 BIN FREE R VALUE SET COUNT : 196 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5832 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.175 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.156 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.669 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6132 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8381 ; 1.440 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 948 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4634 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3094 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4216 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 569 ; 0.139 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 80 ; 0.174 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.203 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4071 ; 0.729 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6358 ; 1.119 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2374 ; 2.106 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2012 ; 3.224 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 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 REMARK 4 REMARK 4 2Z9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000027702. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.05 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58804 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.37900 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: NULL REMARK 200 STARTING MODEL: PDB ID 1VJO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 2M AMMONIUM SULFATE, PH REMARK 280 8.05, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 155.81750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.27250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.27250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 233.72625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.27250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.27250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 77.90875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.27250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.27250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 233.72625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.27250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.27250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 77.90875 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 155.81750 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 17630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 48190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -261.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 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 HIS A 66 56.12 -104.53 REMARK 500 LYS A 197 -102.43 -120.32 REMARK 500 THR B 32 126.61 -36.49 REMARK 500 HIS B 66 54.38 -102.92 REMARK 500 LYS B 197 -104.80 -117.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 951 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 953 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 952 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 954 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z9V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYRIDOXAMINE-PYRUVATE AMINOTRANSFERASE REMARK 900 COMPLEXED WITH PYRIDOXAMINE REMARK 900 RELATED ID: 2Z9W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYRIDOXAMINE-PYRUVATE AMINOTRANSFERASE REMARK 900 COMPLEXED WITH PYRIDOXAL REMARK 900 RELATED ID: 2Z9X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYRIDOXAMINE-PYRUVATE AMINOTRANSFERASE REMARK 900 COMPLEXED WITH PYRIDOXYL-L-ALANINE DBREF 2Z9U A 2 393 UNP Q988B8 Q988B8_RHILO 2 393 DBREF 2Z9U B 2 393 UNP Q988B8 Q988B8_RHILO 2 393 SEQRES 1 A 392 MET ARG TYR PRO GLU HIS ALA ASP PRO VAL ILE THR LEU SEQRES 2 A 392 THR ALA GLY PRO VAL ASN ALA TYR PRO GLU VAL LEU ARG SEQRES 3 A 392 GLY LEU GLY ARG THR VAL LEU TYR ASP TYR ASP PRO ALA SEQRES 4 A 392 PHE GLN LEU LEU TYR GLU LYS VAL VAL ASP LYS ALA GLN SEQRES 5 A 392 LYS ALA MET ARG LEU SER ASN LYS PRO VAL ILE LEU HIS SEQRES 6 A 392 GLY GLU PRO VAL LEU GLY LEU GLU ALA ALA ALA ALA SER SEQRES 7 A 392 LEU ILE SER PRO ASP ASP VAL VAL LEU ASN LEU ALA SER SEQRES 8 A 392 GLY VAL TYR GLY LYS GLY PHE GLY TYR TRP ALA LYS ARG SEQRES 9 A 392 TYR SER PRO HIS LEU LEU GLU ILE GLU VAL PRO TYR ASN SEQRES 10 A 392 GLU ALA ILE ASP PRO GLN ALA VAL ALA ASP MET LEU LYS SEQRES 11 A 392 ALA HIS PRO GLU ILE THR VAL VAL SER VAL CYS HIS HIS SEQRES 12 A 392 ASP THR PRO SER GLY THR ILE ASN PRO ILE ASP ALA ILE SEQRES 13 A 392 GLY ALA LEU VAL SER ALA HIS GLY ALA TYR LEU ILE VAL SEQRES 14 A 392 ASP ALA VAL SER SER PHE GLY GLY MET LYS THR HIS PRO SEQRES 15 A 392 GLU ASP CYS LYS ALA ASP ILE TYR VAL THR GLY PRO ASN SEQRES 16 A 392 LYS CYS LEU GLY ALA PRO PRO GLY LEU THR MET MET GLY SEQRES 17 A 392 VAL SER GLU ARG ALA TRP ALA LYS MET LYS ALA ASN PRO SEQRES 18 A 392 LEU ALA PRO ARG ALA SER MET LEU SER ILE VAL ASP TRP SEQRES 19 A 392 GLU ASN ALA TRP SER ARG ASP LYS PRO PHE PRO PHE THR SEQRES 20 A 392 PRO SER VAL SER GLU ILE ASN GLY LEU ASP VAL ALA LEU SEQRES 21 A 392 ASP LEU TYR LEU ASN GLU GLY PRO GLU ALA VAL TRP ALA SEQRES 22 A 392 ARG HIS ALA LEU THR ALA LYS ALA MET ARG ALA GLY VAL SEQRES 23 A 392 THR ALA MET GLY LEU SER VAL TRP ALA ALA SER ASP SER SEQRES 24 A 392 ILE ALA SER PRO THR THR THR ALA VAL ARG THR PRO ASP SEQRES 25 A 392 GLY VAL ASP GLU LYS ALA LEU ARG GLN ALA ALA ARG ALA SEQRES 26 A 392 ARG TYR GLY VAL VAL PHE SER SER GLY ARG GLY GLU THR SEQRES 27 A 392 LEU GLY LYS LEU THR ARG ILE GLY HIS MET GLY PRO THR SEQRES 28 A 392 ALA GLN PRO ILE TYR ALA ILE ALA ALA LEU THR ALA LEU SEQRES 29 A 392 GLY GLY ALA MET ASN ALA ALA GLY ARG LYS LEU ALA ILE SEQRES 30 A 392 GLY LYS GLY ILE GLU ALA ALA LEU ALA VAL ILE ASP ALA SEQRES 31 A 392 ASP ALA SEQRES 1 B 392 MET ARG TYR PRO GLU HIS ALA ASP PRO VAL ILE THR LEU SEQRES 2 B 392 THR ALA GLY PRO VAL ASN ALA TYR PRO GLU VAL LEU ARG SEQRES 3 B 392 GLY LEU GLY ARG THR VAL LEU TYR ASP TYR ASP PRO ALA SEQRES 4 B 392 PHE GLN LEU LEU TYR GLU LYS VAL VAL ASP LYS ALA GLN SEQRES 5 B 392 LYS ALA MET ARG LEU SER ASN LYS PRO VAL ILE LEU HIS SEQRES 6 B 392 GLY GLU PRO VAL LEU GLY LEU GLU ALA ALA ALA ALA SER SEQRES 7 B 392 LEU ILE SER PRO ASP ASP VAL VAL LEU ASN LEU ALA SER SEQRES 8 B 392 GLY VAL TYR GLY LYS GLY PHE GLY TYR TRP ALA LYS ARG SEQRES 9 B 392 TYR SER PRO HIS LEU LEU GLU ILE GLU VAL PRO TYR ASN SEQRES 10 B 392 GLU ALA ILE ASP PRO GLN ALA VAL ALA ASP MET LEU LYS SEQRES 11 B 392 ALA HIS PRO GLU ILE THR VAL VAL SER VAL CYS HIS HIS SEQRES 12 B 392 ASP THR PRO SER GLY THR ILE ASN PRO ILE ASP ALA ILE SEQRES 13 B 392 GLY ALA LEU VAL SER ALA HIS GLY ALA TYR LEU ILE VAL SEQRES 14 B 392 ASP ALA VAL SER SER PHE GLY GLY MET LYS THR HIS PRO SEQRES 15 B 392 GLU ASP CYS LYS ALA ASP ILE TYR VAL THR GLY PRO ASN SEQRES 16 B 392 LYS CYS LEU GLY ALA PRO PRO GLY LEU THR MET MET GLY SEQRES 17 B 392 VAL SER GLU ARG ALA TRP ALA LYS MET LYS ALA ASN PRO SEQRES 18 B 392 LEU ALA PRO ARG ALA SER MET LEU SER ILE VAL ASP TRP SEQRES 19 B 392 GLU ASN ALA TRP SER ARG ASP LYS PRO PHE PRO PHE THR SEQRES 20 B 392 PRO SER VAL SER GLU ILE ASN GLY LEU ASP VAL ALA LEU SEQRES 21 B 392 ASP LEU TYR LEU ASN GLU GLY PRO GLU ALA VAL TRP ALA SEQRES 22 B 392 ARG HIS ALA LEU THR ALA LYS ALA MET ARG ALA GLY VAL SEQRES 23 B 392 THR ALA MET GLY LEU SER VAL TRP ALA ALA SER ASP SER SEQRES 24 B 392 ILE ALA SER PRO THR THR THR ALA VAL ARG THR PRO ASP SEQRES 25 B 392 GLY VAL ASP GLU LYS ALA LEU ARG GLN ALA ALA ARG ALA SEQRES 26 B 392 ARG TYR GLY VAL VAL PHE SER SER GLY ARG GLY GLU THR SEQRES 27 B 392 LEU GLY LYS LEU THR ARG ILE GLY HIS MET GLY PRO THR SEQRES 28 B 392 ALA GLN PRO ILE TYR ALA ILE ALA ALA LEU THR ALA LEU SEQRES 29 B 392 GLY GLY ALA MET ASN ALA ALA GLY ARG LYS LEU ALA ILE SEQRES 30 B 392 GLY LYS GLY ILE GLU ALA ALA LEU ALA VAL ILE ASP ALA SEQRES 31 B 392 ASP ALA HET SO4 A1601 5 HET SO4 A1602 5 HET SO4 A1603 5 HET GOL A 951 6 HET GOL A 953 6 HET SO4 B2601 5 HET SO4 B2602 5 HET SO4 B2604 5 HET GOL B 952 6 HET GOL B 954 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 6(O4 S 2-) FORMUL 6 GOL 4(C3 H8 O3) FORMUL 13 HOH *550(H2 O) HELIX 1 1 TYR A 22 LEU A 29 1 8 HELIX 2 2 ASP A 38 MET A 56 1 19 HELIX 3 3 PRO A 69 ILE A 81 1 13 HELIX 4 4 GLY A 93 SER A 107 1 15 HELIX 5 5 ASP A 122 HIS A 133 1 12 HELIX 6 6 THR A 146 GLY A 149 5 4 HELIX 7 7 PRO A 153 HIS A 164 1 12 HELIX 8 8 SER A 211 ASN A 221 1 11 HELIX 9 9 ILE A 232 GLU A 236 5 5 HELIX 10 10 SER A 250 GLY A 268 1 19 HELIX 11 11 GLY A 268 GLY A 291 1 24 HELIX 12 12 SER A 298 ALA A 302 5 5 HELIX 13 13 ASP A 316 GLY A 329 1 14 HELIX 14 14 ARG A 336 LEU A 340 5 5 HELIX 15 15 MET A 349 ALA A 353 5 5 HELIX 16 16 GLN A 354 ALA A 372 1 19 HELIX 17 17 ALA A 377 ALA A 393 1 17 HELIX 18 18 TYR B 22 LEU B 29 1 8 HELIX 19 19 ASP B 38 MET B 56 1 19 HELIX 20 20 PRO B 69 ILE B 81 1 13 HELIX 21 21 GLY B 93 SER B 107 1 15 HELIX 22 22 ASP B 122 HIS B 133 1 12 HELIX 23 23 ASP B 145 GLY B 149 5 5 HELIX 24 24 PRO B 153 GLY B 165 1 13 HELIX 25 25 HIS B 182 CYS B 186 5 5 HELIX 26 26 SER B 211 ASN B 221 1 11 HELIX 27 27 ILE B 232 GLU B 236 5 5 HELIX 28 28 SER B 250 GLY B 268 1 19 HELIX 29 29 GLY B 268 GLY B 291 1 24 HELIX 30 30 SER B 298 ALA B 302 5 5 HELIX 31 31 ASP B 316 GLY B 329 1 14 HELIX 32 32 ARG B 336 LEU B 340 5 5 HELIX 33 33 MET B 349 ALA B 353 5 5 HELIX 34 34 GLN B 354 ALA B 372 1 19 HELIX 35 35 ALA B 377 ASP B 392 1 16 SHEET 1 A 2 ILE A 12 THR A 13 0 SHEET 2 A 2 VAL A 330 VAL A 331 1 O VAL A 331 N ILE A 12 SHEET 1 B 7 VAL A 63 LEU A 65 0 SHEET 2 B 7 THR A 206 VAL A 210 -1 O MET A 208 N VAL A 63 SHEET 3 B 7 ILE A 190 THR A 193 -1 N TYR A 191 O GLY A 209 SHEET 4 B 7 TYR A 167 ASP A 171 1 N VAL A 170 O ILE A 190 SHEET 5 B 7 VAL A 138 CYS A 142 1 N VAL A 139 O TYR A 167 SHEET 6 B 7 VAL A 87 ALA A 91 1 N LEU A 88 O VAL A 138 SHEET 7 B 7 LEU A 110 GLU A 114 1 O LEU A 111 N VAL A 87 SHEET 1 C 2 HIS A 144 ASP A 145 0 SHEET 2 C 2 THR A 150 ILE A 151 -1 O THR A 150 N ASP A 145 SHEET 1 D 3 THR A 306 ARG A 310 0 SHEET 2 D 3 LEU A 343 GLY A 347 -1 O ILE A 346 N THR A 307 SHEET 3 D 3 SER A 333 SER A 334 -1 N SER A 333 O ARG A 345 SHEET 1 E 2 ILE B 12 THR B 13 0 SHEET 2 E 2 VAL B 330 VAL B 331 1 O VAL B 331 N ILE B 12 SHEET 1 F 7 VAL B 63 LEU B 65 0 SHEET 2 F 7 THR B 206 VAL B 210 -1 O MET B 208 N VAL B 63 SHEET 3 F 7 ILE B 190 THR B 193 -1 N THR B 193 O MET B 207 SHEET 4 F 7 TYR B 167 ASP B 171 1 N VAL B 170 O ILE B 190 SHEET 5 F 7 VAL B 138 CYS B 142 1 N VAL B 139 O TYR B 167 SHEET 6 F 7 VAL B 87 ALA B 91 1 N LEU B 88 O VAL B 138 SHEET 7 F 7 LEU B 110 GLU B 114 1 O LEU B 111 N VAL B 87 SHEET 1 G 3 THR B 306 ARG B 310 0 SHEET 2 G 3 LEU B 343 GLY B 347 -1 O THR B 344 N VAL B 309 SHEET 3 G 3 SER B 333 SER B 334 -1 N SER B 333 O ARG B 345 CISPEP 1 GLY A 17 PRO A 18 0 -8.99 CISPEP 2 GLY B 17 PRO B 18 0 -7.95 SITE 1 AC1 10 TYR A 95 THR A 146 PRO A 147 LYS A 197 SITE 2 AC1 10 ARG A 336 ARG A 345 GOL A 951 HOH A1609 SITE 3 AC1 10 HOH A1691 HOH A1830 SITE 1 AC2 3 PRO A 5 GLU A 6 HIS A 7 SITE 1 AC3 5 LYS A 219 ARG A 226 HOH A1635 HOH A1747 SITE 2 AC3 5 HOH A1809 SITE 1 AC4 9 TYR B 95 THR B 146 PRO B 147 LYS B 197 SITE 2 AC4 9 ARG B 336 ARG B 345 GOL B 952 HOH B2628 SITE 3 AC4 9 HOH B2668 SITE 1 AC5 4 ARG B 3 PRO B 5 GLU B 6 HIS B 7 SITE 1 AC6 7 ARG B 310 PRO B 312 ASP B 313 ARG B 374 SITE 2 AC6 7 HOH B2678 HOH B2720 HOH B2805 SITE 1 AC7 10 TYR A 95 HIS A 144 THR A 146 ASP A 171 SITE 2 AC7 10 VAL A 173 SER A 174 LYS A 197 SO4 A1601 SITE 3 AC7 10 HOH A1669 HOH A1864 SITE 1 AC8 2 ASP A 299 SER A 300 SITE 1 AC9 10 TYR B 95 HIS B 144 THR B 146 ASP B 171 SITE 2 AC9 10 VAL B 173 SER B 174 LYS B 197 SO4 B2601 SITE 3 AC9 10 HOH B2609 HOH B2756 SITE 1 BC1 3 SER B 298 ASP B 299 SER B 300 CRYST1 68.545 68.545 311.635 90.00 90.00 90.00 P 43 21 2 16 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 0.014589 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003209 0.00000