HEADER OXIDOREDUCTASE 04-AUG-10 3ALJ TITLE CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID TITLE 2 OXYGENASE, REDUCED FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID OXYGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.14.12.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESORHIZOBIUM LOTI; SOURCE 3 ORGANISM_COMMON: MESORHIZOBIUM LOTI; SOURCE 4 ORGANISM_TAXID: 266835; SOURCE 5 STRAIN: MAFF303099; SOURCE 6 GENE: MLR6788; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS ALPHA/BETA FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.KOBAYASHI,H.YOSHIDA,Y.YOSHIKANE,S.KAMITORI,T.YAGI REVDAT 2 01-NOV-23 3ALJ 1 REMARK REVDAT 1 10-AUG-11 3ALJ 0 JRNL AUTH J.KOBAYASHI,H.YOSHIDA,Y.YOSHIKANE,S.KAMITORI,T.YAGI JRNL TITL CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC JRNL TITL 2 ACID OXYGENASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 70377 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3567 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 257 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2866 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 103 REMARK 3 SOLVENT ATOMS : 277 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00700 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : -0.00200 REMARK 3 B13 (A**2) : -0.00400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.030 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 2.608 ; NULL 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): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3ALJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000029398. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI-SINGLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70553 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.36300 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: PDB ENTRY 3ALH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL PH 8.5, 8% PEG 8000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.46150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.39400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 66.47200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.46150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.39400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 66.47200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.46150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.39400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 66.47200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.46150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.39400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 66.47200 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 300 REMARK: BIOLOGICAL UNIT IS TETRAMER, BUT SPECIFIC INTERACTION WAS REMARK 300 NOT OBSERVED. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 475 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 ALA A 2 REMARK 465 ASN A 3 REMARK 465 VAL A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 6 REMARK 465 THR A 7 REMARK 465 PRO A 8 REMARK 465 GLY A 9 REMARK 465 LYS A 10 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 SG CYS A 303 S2 BME A 382 1.92 REMARK 500 SG CYS A 294 S2 BME A 381 2.05 REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 37 CB VAL A 37 CG2 -0.142 REMARK 500 MET A 248 CB MET A 248 CG 0.251 REMARK 500 ARG A 333 CD ARG A 333 NE -0.106 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 12 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 38 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 47 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP A 111 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 111 CB - CG - OD2 ANGL. DEV. = -11.1 DEGREES REMARK 500 ARG A 118 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 150 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 156 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 163 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 163 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 172 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 186 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 186 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP A 197 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 208 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 208 NE - CZ - NH1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 208 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP A 232 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 LEU A 275 CB - CG - CD2 ANGL. DEV. = 11.6 DEGREES REMARK 500 ASP A 314 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 LEU A 325 CB - CG - CD1 ANGL. DEV. = 11.5 DEGREES REMARK 500 TYR A 346 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 350 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 367 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 373 NH1 - CZ - NH2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG A 373 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 51 -76.15 70.64 REMARK 500 GLU A 195 67.39 -119.04 REMARK 500 ASN A 218 -172.20 -177.19 REMARK 500 HIS A 291 42.37 -151.70 REMARK 500 SER A 376 -169.90 -121.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 198 THR A 199 149.56 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 FAD A 380 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 382 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 383 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 384 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 385 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 386 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 387 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 388 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 389 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ALH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID REMARK 900 OXYGENASE, FREE FORM REMARK 900 RELATED ID: 3ALI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID REMARK 900 OXYGENASE, 5-PYRIDOXIC ACID BOUND FORM REMARK 900 RELATED ID: 3ALK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID REMARK 900 OXYGENASE, MUTANT Y270F REMARK 900 RELATED ID: 3ALL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID REMARK 900 OXYGENASE, MUTANT Y270A REMARK 900 RELATED ID: 3ALM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID REMARK 900 OXYGENASE, MUTANT C294A DBREF 3ALJ A 1 379 UNP Q988D3 Q988D3_RHILO 1 379 SEQRES 1 A 379 MET ALA ASN VAL ASN LYS THR PRO GLY LYS THR ARG ARG SEQRES 2 A 379 ALA GLU VAL ALA GLY GLY GLY PHE ALA GLY LEU THR ALA SEQRES 3 A 379 ALA ILE ALA LEU LYS GLN ASN GLY TRP ASP VAL ARG LEU SEQRES 4 A 379 HIS GLU LYS SER SER GLU LEU ARG ALA PHE GLY ALA GLY SEQRES 5 A 379 ILE TYR LEU TRP HIS ASN GLY LEU ARG VAL LEU GLU GLY SEQRES 6 A 379 LEU GLY ALA LEU ASP ASP VAL LEU GLN GLY SER HIS THR SEQRES 7 A 379 PRO PRO THR TYR GLU THR TRP MET HIS ASN LYS SER VAL SEQRES 8 A 379 SER LYS GLU THR PHE ASN GLY LEU PRO TRP ARG ILE MET SEQRES 9 A 379 THR ARG SER HIS LEU HIS ASP ALA LEU VAL ASN ARG ALA SEQRES 10 A 379 ARG ALA LEU GLY VAL ASP ILE SER VAL ASN SER GLU ALA SEQRES 11 A 379 VAL ALA ALA ASP PRO VAL GLY ARG LEU THR LEU GLN THR SEQRES 12 A 379 GLY GLU VAL LEU GLU ALA ASP LEU ILE VAL GLY ALA ASP SEQRES 13 A 379 GLY VAL GLY SER LYS VAL ARG ASP SER ILE GLY PHE LYS SEQRES 14 A 379 GLN ASP ARG TRP VAL SER LYS ASP GLY LEU ILE ARG LEU SEQRES 15 A 379 ILE VAL PRO ARG MET LYS LYS GLU LEU GLY HIS GLY GLU SEQRES 16 A 379 TRP ASP ASN THR ILE ASP MET TRP ASN PHE TRP PRO ARG SEQRES 17 A 379 VAL GLN ARG ILE LEU TYR SER PRO CYS ASN GLU ASN GLU SEQRES 18 A 379 LEU TYR LEU GLY LEU MET ALA PRO ALA ALA ASP PRO ARG SEQRES 19 A 379 GLY SER SER VAL PRO ILE ASP LEU GLU VAL TRP VAL GLU SEQRES 20 A 379 MET PHE PRO PHE LEU GLU PRO CYS LEU ILE GLU ALA ALA SEQRES 21 A 379 LYS LEU LYS THR ALA ARG TYR ASP LYS TYR GLU THR THR SEQRES 22 A 379 LYS LEU ASP SER TRP THR ARG GLY LYS VAL ALA LEU VAL SEQRES 23 A 379 GLY ASP ALA ALA HIS ALA MET CYS PRO ALA LEU ALA GLN SEQRES 24 A 379 GLY ALA GLY CYS ALA MET VAL ASN ALA PHE SER LEU SER SEQRES 25 A 379 GLN ASP LEU GLU GLU GLY SER SER VAL GLU ASP ALA LEU SEQRES 26 A 379 VAL ALA TRP GLU THR ARG ILE ARG PRO ILE THR ASP ARG SEQRES 27 A 379 CYS GLN ALA LEU SER GLY ASP TYR ALA ALA ASN ARG SER SEQRES 28 A 379 LEU SER LYS GLY ASN MET PHE THR PRO ALA ALA LEU GLU SEQRES 29 A 379 ALA ALA ARG TYR ASP PRO LEU ARG ARG VAL TYR SER TRP SEQRES 30 A 379 PRO GLN HET FAD A 380 53 HET BME A 381 4 HET BME A 382 4 HET GOL A 383 6 HET GOL A 384 6 HET GOL A 385 6 HET GOL A 386 6 HET GOL A 387 6 HET GOL A 388 6 HET GOL A 389 6 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM BME BETA-MERCAPTOETHANOL HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 BME 2(C2 H6 O S) FORMUL 5 GOL 7(C3 H8 O3) FORMUL 12 HOH *277(H2 O) HELIX 1 1 GLY A 20 ASN A 33 1 14 HELIX 2 2 HIS A 57 LEU A 66 1 10 HELIX 3 3 ALA A 68 GLN A 74 1 7 HELIX 4 4 THR A 95 LEU A 99 5 5 HELIX 5 5 ARG A 106 LEU A 120 1 15 HELIX 6 6 SER A 160 GLY A 167 1 8 HELIX 7 7 MET A 187 GLY A 192 1 6 HELIX 8 8 ASP A 241 PHE A 249 1 9 HELIX 9 9 LEU A 252 LYS A 261 1 10 HELIX 10 10 GLY A 287 ALA A 292 1 6 HELIX 11 11 CYS A 294 ALA A 298 5 5 HELIX 12 12 GLN A 299 LEU A 315 1 17 HELIX 13 13 SER A 320 ARG A 350 1 31 HELIX 14 14 SER A 351 GLY A 355 5 5 HELIX 15 15 LEU A 363 ARG A 367 1 5 SHEET 1 A 6 ASP A 123 SER A 125 0 SHEET 2 A 6 ASP A 36 HIS A 40 1 N LEU A 39 O ASP A 123 SHEET 3 A 6 ARG A 13 ALA A 17 1 N VAL A 16 O HIS A 40 SHEET 4 A 6 LEU A 151 GLY A 154 1 O VAL A 153 N ALA A 17 SHEET 5 A 6 VAL A 283 LEU A 285 1 O ALA A 284 N GLY A 154 SHEET 6 A 6 THR A 279 ARG A 280 -1 N ARG A 280 O VAL A 283 SHEET 1 B 2 GLY A 52 TRP A 56 0 SHEET 2 B 2 TRP A 101 THR A 105 -1 O ARG A 102 N LEU A 55 SHEET 1 C 7 LYS A 89 GLU A 94 0 SHEET 2 C 7 TYR A 82 MET A 86 -1 N THR A 84 O VAL A 91 SHEET 3 C 7 THR A 199 TRP A 203 1 O ASP A 201 N TRP A 85 SHEET 4 C 7 ARG A 211 PRO A 216 -1 O ILE A 212 N MET A 202 SHEET 5 C 7 GLU A 221 ALA A 228 -1 O MET A 227 N ARG A 211 SHEET 6 C 7 GLN A 170 PRO A 185 -1 N ILE A 180 O LEU A 226 SHEET 7 C 7 TYR A 267 LEU A 275 -1 O THR A 272 N TRP A 173 SHEET 1 D 3 ALA A 130 ASP A 134 0 SHEET 2 D 3 ARG A 138 LEU A 141 -1 O THR A 140 N VAL A 131 SHEET 3 D 3 VAL A 146 GLU A 148 -1 O LEU A 147 N LEU A 139 SHEET 1 E 2 TYR A 368 ASP A 369 0 SHEET 2 E 2 VAL A 374 TYR A 375 -1 O VAL A 374 N ASP A 369 CISPEP 1 TRP A 206 PRO A 207 0 1.93 CISPEP 2 VAL A 238 PRO A 239 0 -8.09 SITE 1 AC1 38 GLY A 18 GLY A 20 PHE A 21 ALA A 22 SITE 2 AC1 38 HIS A 40 GLU A 41 LYS A 42 SER A 43 SITE 3 AC1 38 ILE A 53 TYR A 54 ARG A 106 SER A 128 SITE 4 AC1 38 GLU A 129 ALA A 130 ALA A 155 ASP A 156 SITE 5 AC1 38 LEU A 179 ARG A 181 GLY A 287 ASP A 288 SITE 6 AC1 38 PRO A 295 ALA A 298 GLY A 300 ALA A 301 SITE 7 AC1 38 GLY A 302 HOH A 390 HOH A 394 HOH A 402 SITE 8 AC1 38 HOH A 405 HOH A 408 HOH A 431 HOH A 439 SITE 9 AC1 38 HOH A 506 HOH A 513 HOH A 535 HOH A 570 SITE 10 AC1 38 HOH A 583 HOH A 617 SITE 1 AC2 6 GLN A 142 TYR A 270 CYS A 294 ALA A 347 SITE 2 AC2 6 GOL A 386 HOH A 529 SITE 1 AC3 7 ASN A 58 CYS A 303 VAL A 306 ILE A 335 SITE 2 AC3 7 THR A 336 ALA A 365 TYR A 368 SITE 1 AC4 6 LYS A 169 GLN A 170 ASP A 171 LYS A 274 SITE 2 AC4 6 ASP A 276 HOH A 443 SITE 1 AC5 10 LYS A 42 GLU A 129 LYS A 161 LYS A 274 SITE 2 AC5 10 GLN A 340 HOH A 443 HOH A 470 HOH A 499 SITE 3 AC5 10 HOH A 540 HOH A 542 SITE 1 AC6 5 TRP A 85 ASN A 88 LYS A 89 PHE A 251 SITE 2 AC6 5 HOH A 543 SITE 1 AC7 12 ARG A 211 TYR A 270 CYS A 294 PRO A 295 SITE 2 AC7 12 ALA A 296 ALA A 347 BME A 381 HOH A 432 SITE 3 AC7 12 HOH A 474 HOH A 525 HOH A 590 HOH A 623 SITE 1 AC8 6 GLN A 74 GLY A 75 SER A 76 ASN A 97 SITE 2 AC8 6 GLU A 219 HOH A 666 SITE 1 AC9 5 HIS A 57 LEU A 60 ARG A 61 GLU A 64 SITE 2 AC9 5 HOH A 603 SITE 1 BC1 3 GLU A 364 ARG A 367 TYR A 375 CRYST1 48.923 130.788 132.944 90.00 90.00 90.00 I 2 2 2 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 0.020440 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007522 0.00000