HEADER TRANSFERASE 26-SEP-07 2Z9X TITLE CRYSTAL STRUCTURE OF PYRIDOXAMINE-PYRUVATE AMINOTRANSFERASE COMPLEXED TITLE 2 WITH PYRIDOXYL-L-ALANINE 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, ALANINE, 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 2Z9X 1 REMARK LINK REVDAT 4 13-JUL-11 2Z9X 1 VERSN REVDAT 3 24-FEB-09 2Z9X 1 VERSN REVDAT 2 03-JUN-08 2Z9X 1 JRNL REVDAT 1 06-NOV-07 2Z9X 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. 1.94 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 52891 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) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2827 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) : 1.94 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.99 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3677 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.1570 REMARK 3 BIN FREE R VALUE SET COUNT : 208 REMARK 3 BIN FREE R VALUE : 0.2220 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 : 136 REMARK 3 SOLVENT ATOMS : 614 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.26 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): 0.147 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.677 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6323 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8658 ; 1.342 ; 1.989 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): 969 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4798 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3163 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4337 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 556 ; 0.143 ; 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): 81 ; 0.180 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 38 ; 0.151 ; 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): 4138 ; 0.687 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6481 ; 1.039 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2514 ; 1.982 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2148 ; 3.060 ; 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 2Z9X 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_1000027705. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 56030 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.940 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 (%) : 98.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.94 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 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 2Z9U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 2M AMMONIUM SULFATE, 5MM REMARK 280 PYRIDOXYL-L-ALANINE, PH 8.05, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 155.97100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.36000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.36000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 233.95650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.36000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.36000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 77.98550 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.36000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.36000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 233.95650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.36000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.36000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 77.98550 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 155.97100 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: 24590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -363.0 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 58.55 -100.58 REMARK 500 LYS A 197 -104.13 -114.08 REMARK 500 HIS B 66 56.92 -103.33 REMARK 500 LYS B 197 -105.31 -117.96 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 1602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1606 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 SO4 B 2605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 2606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1608 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 2608 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ALA A 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXL A 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ALA B 2502 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXL B 2503 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 953 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 954 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 955 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 956 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 957 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 958 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 959 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 960 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 961 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 962 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z9U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RECOMBINANT PYRIDOXAMINE-PYRUVATE REMARK 900 AMINOTRANSFERASE FROM MESORHIZOBIUM LOTI AT 2.0 A RESOLUTION 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: 2Z9V RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PYRIDOXAMINE-PYRUVATE AMINOTRANSFERASE REMARK 900 COMPLEXED WITH PYRIDOXAMINE DBREF 2Z9X A 2 393 UNP Q988B8 Q988B8_RHILO 2 393 DBREF 2Z9X 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 A1602 5 HET SO4 A1603 5 HET SO4 A1605 5 HET SO4 A1606 5 HET CL A1608 1 HET ALA A1502 6 HET PXL A1503 11 HET GOL A 953 6 HET GOL A 955 6 HET GOL A 957 6 HET GOL A 959 6 HET SO4 B2602 5 HET SO4 B2604 5 HET SO4 B2605 5 HET SO4 B2606 5 HET CL B2608 1 HET ALA B2502 6 HET PXL B2503 11 HET GOL B 954 6 HET GOL B 956 6 HET GOL B 958 6 HET GOL B 960 6 HET GOL B 961 6 HET GOL B 962 6 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM ALA ALANINE HETNAM PXL 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE HETNAM GOL GLYCEROL HETSYN PXL PYRIDOXAL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 8(O4 S 2-) FORMUL 7 CL 2(CL 1-) FORMUL 8 ALA 2(C3 H7 N O2) FORMUL 9 PXL 2(C8 H9 N O3) FORMUL 10 GOL 10(C3 H8 O3) FORMUL 27 HOH *614(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 ASP A 145 GLY A 149 5 5 HELIX 7 7 PRO A 153 HIS A 164 1 12 HELIX 8 8 HIS A 182 LYS A 187 5 6 HELIX 9 9 SER A 211 ALA A 220 1 10 HELIX 10 10 ILE A 232 GLU A 236 5 5 HELIX 11 11 SER A 250 GLY A 268 1 19 HELIX 12 12 GLY A 268 GLY A 291 1 24 HELIX 13 13 SER A 298 ALA A 302 5 5 HELIX 14 14 ASP A 316 GLY A 329 1 14 HELIX 15 15 ARG A 336 LEU A 340 5 5 HELIX 16 16 MET A 349 ALA A 353 5 5 HELIX 17 17 GLN A 354 ALA A 372 1 19 HELIX 18 18 ALA A 377 ASP A 392 1 16 HELIX 19 19 TYR B 22 LEU B 29 1 8 HELIX 20 20 ASP B 38 MET B 56 1 19 HELIX 21 21 PRO B 69 ILE B 81 1 13 HELIX 22 22 GLY B 93 SER B 107 1 15 HELIX 23 23 ASP B 122 HIS B 133 1 12 HELIX 24 24 ASP B 145 GLY B 149 5 5 HELIX 25 25 PRO B 153 GLY B 165 1 13 HELIX 26 26 HIS B 182 CYS B 186 5 5 HELIX 27 27 SER B 211 ASN B 221 1 11 HELIX 28 28 ILE B 232 GLU B 236 5 5 HELIX 29 29 SER B 250 GLY B 268 1 19 HELIX 30 30 GLY B 268 GLY B 291 1 24 HELIX 31 31 SER B 298 ALA B 302 5 5 HELIX 32 32 ASP B 316 GLY B 329 1 14 HELIX 33 33 ARG B 336 LEU B 340 5 5 HELIX 34 34 MET B 349 ALA B 353 5 5 HELIX 35 35 GLN B 354 ALA B 372 1 19 HELIX 36 36 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 86 ALA A 91 1 N LEU A 88 O VAL A 138 SHEET 7 B 7 HIS A 109 GLU A 114 1 O LEU A 111 N VAL A 87 SHEET 1 C 3 THR A 306 ARG A 310 0 SHEET 2 C 3 LEU A 343 GLY A 347 -1 O THR A 344 N VAL A 309 SHEET 3 C 3 SER A 333 SER A 334 -1 N SER A 333 O ARG A 345 SHEET 1 D 2 ILE B 12 THR B 13 0 SHEET 2 D 2 VAL B 330 VAL B 331 1 O VAL B 331 N ILE B 12 SHEET 1 E 7 VAL B 63 LEU B 65 0 SHEET 2 E 7 THR B 206 VAL B 210 -1 O MET B 208 N VAL B 63 SHEET 3 E 7 ILE B 190 THR B 193 -1 N THR B 193 O MET B 207 SHEET 4 E 7 TYR B 167 ASP B 171 1 N VAL B 170 O ILE B 190 SHEET 5 E 7 VAL B 138 CYS B 142 1 N VAL B 139 O TYR B 167 SHEET 6 E 7 VAL B 87 ALA B 91 1 N LEU B 88 O VAL B 138 SHEET 7 E 7 LEU B 110 GLU B 114 1 O LEU B 111 N VAL B 87 SHEET 1 F 2 THR B 306 ARG B 310 0 SHEET 2 F 2 LEU B 343 GLY B 347 -1 O THR B 344 N VAL B 309 LINK N ALA A1502 C4A PXL A1503 1555 1555 1.49 LINK N ALA B2502 C4A PXL B2503 1555 1555 1.50 CISPEP 1 GLY A 17 PRO A 18 0 -1.96 CISPEP 2 GLY B 17 PRO B 18 0 -8.58 SITE 1 AC1 3 PRO A 5 GLU A 6 HIS A 7 SITE 1 AC2 5 LYS A 219 ARG A 226 HOH A1714 HOH A1729 SITE 2 AC2 5 HOH A1840 SITE 1 AC3 7 PRO A 23 GLU A 24 ARG A 27 ARG A 31 SITE 2 AC3 7 THR A 32 HOH A1800 HOH B2839 SITE 1 AC4 4 GLU A 24 ARG A 27 ARG A 31 HOH A1883 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 B2699 HOH B2756 HOH B2768 SITE 1 AC7 7 ASP A 9 HOH A1817 PRO B 23 GLU B 24 SITE 2 AC7 7 ARG B 27 ARG B 31 THR B 32 SITE 1 AC8 4 GLU B 24 ARG B 27 ARG B 31 HOH B2825 SITE 1 AC9 3 PRO A 69 ASN A 196 LYS A 197 SITE 1 BC1 6 PRO B 69 GLY B 194 PRO B 195 ASN B 196 SITE 2 BC1 6 LYS B 197 HOH B2665 SITE 1 BC2 7 TYR A 95 THR A 146 ARG A 345 GOL A 957 SITE 2 BC2 7 PXL A1503 HOH A1642 THR B 248 SITE 1 BC3 9 GLU A 68 TYR A 95 HIS A 144 THR A 146 SITE 2 BC3 9 ASP A 171 VAL A 173 LYS A 197 ALA A1502 SITE 3 BC3 9 HOH A1645 SITE 1 BC4 7 THR A 248 TYR B 95 THR B 146 ARG B 345 SITE 2 BC4 7 GOL B 958 PXL B2503 HOH B2622 SITE 1 BC5 9 GLU B 68 TYR B 95 HIS B 144 THR B 146 SITE 2 BC5 9 ASP B 171 VAL B 173 LYS B 197 ALA B2502 SITE 3 BC5 9 HOH B2642 SITE 1 BC6 2 ASP A 299 SER A 300 SITE 1 BC7 3 SER B 298 ASP B 299 SER B 300 SITE 1 BC8 6 VAL A 94 TYR A 95 GLY A 98 ARG A 336 SITE 2 BC8 6 HOH A1630 HOH A1871 SITE 1 BC9 7 VAL B 94 TYR B 95 TRP B 102 ARG B 336 SITE 2 BC9 7 HOH B2736 HOH B2794 HOH B2876 SITE 1 CC1 8 SER A 334 GLY A 335 ARG A 336 ARG A 345 SITE 2 CC1 8 ALA A1502 TYR B 35 TYR B 37 HOH B2676 SITE 1 CC2 9 TYR A 35 TYR A 37 HOH A1613 SER B 334 SITE 2 CC2 9 GLY B 335 ARG B 336 ARG B 345 ALA B2502 SITE 3 CC2 9 HOH B2694 SITE 1 CC3 5 ILE A 12 THR A 13 ASN A 20 PRO A 351 SITE 2 CC3 5 TYR A 357 SITE 1 CC4 5 ILE B 12 THR B 13 ASN B 20 PRO B 351 SITE 2 CC4 5 TYR B 357 SITE 1 CC5 10 VAL A 70 TRP A 102 HOH A1662 ALA B 227 SITE 2 CC5 10 SER B 228 MET B 229 ASP B 234 PHE B 247 SITE 3 CC5 10 HOH B2640 HOH B2701 SITE 1 CC6 5 GLU B 114 LYS B 219 ARG B 226 HOH B2776 SITE 2 CC6 5 HOH B2883 CRYST1 68.720 68.720 311.942 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 0.014552 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014552 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003206 0.00000