HEADER OXIDOREDUCTASE 11-JUL-14 4QUP TITLE CRYSTAL STRUCTURE OF STACHYDRINE DEMETHYLASE WITH N-METHYL PROLINE TITLE 2 FROM LOW X-RAY DOSE COMPOSITE DATASETS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MONOXYGENASE; DEMETHYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: STACHYDRINE DEMETHYLASE; COMPND 5 EC: 1.-.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SINORHIZOBIUM MELILOTI 1021; SOURCE 3 ORGANISM_COMMON: ENSIFER MELILOTI; SOURCE 4 ORGANISM_TAXID: 266834; SOURCE 5 GENE: SMA0751; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSGC KEYWDS COMPOSITE DATASETS, PHOTOELECTRON, ENZYME-CATALYZED REACTIONS, KEYWDS 2 CYANIDE, SYNCHROTRON, RIESKE TYPE MONOXYGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.AGARWAL,B.ANDI,A.GIZZI,J.B.BONANNO,S.C.ALMO,A.M.ORVILLE REVDAT 4 20-SEP-23 4QUP 1 REMARK SEQADV LINK REVDAT 3 09-MAR-16 4QUP 1 AUTHOR JRNL REVDAT 2 14-OCT-15 4QUP 1 ATOM REVDAT 1 15-JUL-15 4QUP 0 JRNL AUTH R.AGARWAL,B.ANDI,A.GIZZI,J.B.BONANNO,S.C.ALMO,A.M.ORVILLE JRNL TITL TRACKING PHOTOELECTRON INDUCED IN-CRYSTALLO ENZYME CATALYSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 52900 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2822 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3783 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 186 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3265 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.01000 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): 0.096 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.063 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.894 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 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): 3388 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3130 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4621 ; 1.923 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7181 ; 1.038 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 412 ; 6.470 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;36.021 ;23.481 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 517 ;13.267 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;15.038 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 495 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3841 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 809 ; 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 REMARK 4 REMARK 4 4QUP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000086536. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55766 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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 3VCA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG3350, 10% GLYCEROL, 100 MM REMARK 280 HEPES, PH 7.0, 25 MM HEXAMMINECOBALT CHLORIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 88.99200 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 88.99200 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 88.99200 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 88.99200 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 88.99200 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 88.99200 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: 12270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 48.87300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 253.95156 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -195.49200 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 169.30104 REMARK 350 BIOMT3 3 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 CO NCO A 506 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 -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 SER A -15 REMARK 465 SER A -14 REMARK 465 GLY A -13 REMARK 465 VAL A -12 REMARK 465 ASP A -11 REMARK 465 LEU A -10 REMARK 465 LEU A 218 REMARK 465 PRO A 406 REMARK 465 ARG A 407 REMARK 465 GLN A 408 REMARK 465 VAL A 409 REMARK 465 ALA A 410 REMARK 465 ALA A 411 REMARK 465 GLU A 412 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A -7 CG CD OE1 OE2 REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 98 CG CD OE1 NE2 REMARK 470 GLU A 268 CG CD OE1 OE2 REMARK 470 LYS A 269 CG CD CE NZ 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 200 NE - CZ - NH2 ANGL. DEV. = -3.0 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 SER A 7 62.64 36.98 REMARK 500 ALA A 47 -71.71 -107.44 REMARK 500 HIS A 88 -78.81 -72.81 REMARK 500 ALA A 249 -33.01 -142.18 REMARK 500 ALA A 254 151.26 -48.37 REMARK 500 GLU A 268 -126.27 49.91 REMARK 500 ASP A 292 32.00 -98.44 REMARK 500 VAL A 342 -57.60 -121.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 86 SG REMARK 620 2 FES A 501 S1 106.5 REMARK 620 3 FES A 501 S2 112.0 106.1 REMARK 620 4 CYS A 106 SG 107.3 110.6 114.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 88 ND1 REMARK 620 2 FES A 501 S1 111.4 REMARK 620 3 FES A 501 S2 113.3 105.4 REMARK 620 4 HIS A 109 ND1 94.1 114.5 118.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 204 NE2 REMARK 620 2 HIS A 209 NE2 92.2 REMARK 620 3 ASP A 360 OD1 96.9 98.7 REMARK 620 4 ASP A 360 OD2 151.4 101.0 56.4 REMARK 620 5 3BY A 503 O 86.7 95.0 165.7 116.8 REMARK 620 6 3BY A 503 OXT 140.4 87.2 122.4 66.2 54.0 REMARK 620 7 HOH A 786 O 103.1 159.6 92.8 71.5 72.9 72.4 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3BY A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NCO A 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VCA RELATED DB: PDB REMARK 900 RELATED ID: 3VCP RELATED DB: PDB REMARK 900 RELATED ID: 4QUQ RELATED DB: PDB REMARK 900 RELATED ID: 4QUR RELATED DB: PDB DBREF 4QUP A 1 412 UNP Q92ZP9 Q92ZP9_RHIME 1 412 SEQADV 4QUP MET A -22 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP HIS A -21 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP HIS A -20 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP HIS A -19 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP HIS A -18 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP HIS A -17 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP HIS A -16 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP SER A -15 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP SER A -14 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP GLY A -13 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP VAL A -12 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP ASP A -11 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP LEU A -10 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP GLY A -9 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP THR A -8 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP GLU A -7 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP ASN A -6 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP LEU A -5 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP TYR A -4 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP PHE A -3 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP GLN A -2 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP SER A -1 UNP Q92ZP9 EXPRESSION TAG SEQADV 4QUP MET A 0 UNP Q92ZP9 EXPRESSION TAG SEQRES 1 A 435 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 435 GLY THR GLU ASN LEU TYR PHE GLN SER MET MET THR ALA SEQRES 3 A 435 ASN PRO THR SER ILE HIS GLN ARG LEU ASP ARG ARG LEU SEQRES 4 A 435 SER GLY PHE SER LEU GLU GLN PRO PHE TYR THR SER PRO SEQRES 5 A 435 GLU VAL TYR ALA LEU ASP LEU GLN HIS ILE PHE TYR LYS SEQRES 6 A 435 GLN TRP LEU TYR ALA VAL PRO VAL CYS GLN LEU ALA LYS SEQRES 7 A 435 ALA GLY SER TYR THR THR LEU ARG VAL GLY ALA TYR GLU SEQRES 8 A 435 VAL VAL ILE VAL ARG SER ARG ASP GLY GLU VAL ARG ALA SEQRES 9 A 435 PHE HIS ASN SER CYS ARG HIS ARG GLY SER LEU ILE CYS SEQRES 10 A 435 LYS ALA ARG GLN GLY GLN VAL ALA LYS LEU VAL CYS PRO SEQRES 11 A 435 TYR HIS GLN TRP THR TYR GLU LEU ASP GLY LYS LEU ILE SEQRES 12 A 435 TRP ALA ASN ASP MET GLY PRO ASP PHE ASP ALA SER LYS SEQRES 13 A 435 TYR GLY LEU LYS PRO VAL ASN LEU ARG ASN LEU ASP GLY SEQRES 14 A 435 LEU ILE TYR ILE CYS LEU SER ASP THR PRO PRO ASP PHE SEQRES 15 A 435 GLN THR PHE ALA GLN LEU ALA ARG PRO TYR LEU GLU VAL SEQRES 16 A 435 HIS ASP LEU LYS ASP ALA LYS VAL ALA PHE THR SER THR SEQRES 17 A 435 ILE ILE GLU LYS GLY ASN TRP LYS LEU VAL TRP GLU ASN SEQRES 18 A 435 ASN ARG GLU CYS TYR HIS CYS SER SER ASN HIS PRO ALA SEQRES 19 A 435 LEU CYS ARG SER PHE PRO LEU ASP PRO GLU VAL ALA GLY SEQRES 20 A 435 VAL GLN ALA ASP GLY GLY VAL SER LYS LYS LEU GLN ALA SEQRES 21 A 435 HIS PHE ASP ARG CYS GLU ALA ALA GLY THR PRO ALA GLN SEQRES 22 A 435 PHE VAL LEU ALA GLY ASP GLY GLN TYR ARG LEU ALA ARG SEQRES 23 A 435 MET PRO LEU GLN GLU LYS ALA LEU SER TYR THR MET ASP SEQRES 24 A 435 GLY LYS ALA ALA VAL SER ARG HIS LEU GLY ARG VAL ALA SEQRES 25 A 435 PRO PRO ASP ALA GLY THR LEU LEU MET PHE HIS TYR PRO SEQRES 26 A 435 SER THR TRP ASN HIS PHE LEU PRO ASP HIS SER LEU THR SEQRES 27 A 435 PHE ARG VAL MET PRO ILE SER PRO THR GLU THR GLU VAL SEQRES 28 A 435 THR THR THR TRP LEU VAL HIS LYS ASP ALA VAL GLU GLY SEQRES 29 A 435 VAL ASP TYR ASP LEU LYS ARG LEU THR GLU VAL TRP ILE SEQRES 30 A 435 ALA THR ASN ASP GLU ASP ARG GLU ILE VAL GLU THR ASN SEQRES 31 A 435 GLN GLN GLY ILE LEU SER PRO ALA TYR VAL PRO GLY PRO SEQRES 32 A 435 TYR SER PRO GLY GLN GLU SER GLY VAL MET GLN PHE VAL SEQRES 33 A 435 ASP TRP TYR ALA ALA SER LEU GLU ARG ALA LEU ALA PRO SEQRES 34 A 435 ARG GLN VAL ALA ALA GLU HET FES A 501 4 HET FE A 502 1 HET 3BY A 503 9 HET TRS A 504 8 HET GOL A 505 6 HET NCO A 506 7 HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETNAM FE FE (III) ION HETNAM 3BY 1-METHYL-L-PROLINE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM GOL GLYCEROL HETNAM NCO COBALT HEXAMMINE(III) HETSYN TRS TRIS BUFFER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FES FE2 S2 FORMUL 3 FE FE 3+ FORMUL 4 3BY C6 H11 N O2 FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 GOL C3 H8 O3 FORMUL 7 NCO CO H18 N6 3+ FORMUL 8 HOH *260(H2 O) HELIX 1 1 GLY A -9 ALA A 3 1 13 HELIX 2 2 SER A 7 ARG A 15 1 9 HELIX 3 3 GLU A 22 SER A 28 1 7 HELIX 4 4 SER A 28 ILE A 39 1 12 HELIX 5 5 CYS A 51 ALA A 54 5 4 HELIX 6 6 ASP A 130 TYR A 134 5 5 HELIX 7 7 PHE A 159 VAL A 172 1 14 HELIX 8 8 HIS A 173 LYS A 176 5 4 HELIX 9 9 ASN A 191 ARG A 200 1 10 HELIX 10 10 HIS A 204 HIS A 209 1 6 HELIX 11 11 HIS A 209 ARG A 214 1 6 HELIX 12 12 PRO A 220 GLY A 224 1 5 HELIX 13 13 VAL A 225 GLY A 230 5 6 HELIX 14 14 SER A 232 ALA A 245 1 14 HELIX 15 15 ASP A 345 LEU A 372 1 28 HELIX 16 16 GLU A 386 ALA A 405 1 20 SHEET 1 A 7 LEU A 45 PRO A 49 0 SHEET 2 A 7 LEU A 147 CYS A 151 -1 O ILE A 148 N ALA A 47 SHEET 3 A 7 PRO A 138 LEU A 144 -1 N LEU A 144 O LEU A 147 SHEET 4 A 7 VAL A 79 HIS A 83 -1 N ALA A 81 O VAL A 139 SHEET 5 A 7 TYR A 67 ARG A 73 -1 N VAL A 72 O ARG A 80 SHEET 6 A 7 SER A 58 VAL A 64 -1 N THR A 60 O ILE A 71 SHEET 7 A 7 GLN A 98 GLN A 100 -1 O GLY A 99 N TYR A 59 SHEET 1 B 3 LEU A 104 VAL A 105 0 SHEET 2 B 3 THR A 112 TYR A 113 -1 O TYR A 113 N LEU A 104 SHEET 3 B 3 LEU A 119 TRP A 121 -1 O TRP A 121 N THR A 112 SHEET 1 C 7 ALA A 178 GLU A 188 0 SHEET 2 C 7 GLU A 325 HIS A 335 -1 O THR A 330 N SER A 184 SHEET 3 C 7 SER A 313 SER A 322 -1 N SER A 313 O LEU A 333 SHEET 4 C 7 THR A 304 PHE A 308 -1 N HIS A 307 O LEU A 314 SHEET 5 C 7 THR A 295 HIS A 300 -1 N LEU A 296 O PHE A 308 SHEET 6 C 7 TYR A 259 MET A 264 -1 N ALA A 262 O LEU A 297 SHEET 7 C 7 VAL A 252 LEU A 253 -1 N VAL A 252 O LEU A 261 SSBOND 1 CYS A 202 CYS A 205 1555 1555 2.07 LINK SG CYS A 86 FE2 FES A 501 1555 1555 2.35 LINK ND1 HIS A 88 FE1 FES A 501 1555 1555 2.18 LINK SG CYS A 106 FE2 FES A 501 1555 1555 2.29 LINK ND1 HIS A 109 FE1 FES A 501 1555 1555 2.16 LINK NE2 HIS A 204 FE FE A 502 1555 1555 2.11 LINK NE2 HIS A 209 FE FE A 502 1555 1555 2.12 LINK OD1 ASP A 360 FE FE A 502 1555 1555 1.82 LINK OD2 ASP A 360 FE FE A 502 1555 1555 2.62 LINK FE FE A 502 O 3BY A 503 1555 1555 2.41 LINK FE FE A 502 OXT 3BY A 503 1555 1555 2.60 LINK FE FE A 502 O HOH A 786 1555 1555 2.06 CISPEP 1 ALA A 289 PRO A 290 0 1.50 CISPEP 2 TYR A 301 PRO A 302 0 7.04 SITE 1 AC1 6 CYS A 86 HIS A 88 ARG A 89 CYS A 106 SITE 2 AC1 6 HIS A 109 TRP A 111 SITE 1 AC2 5 HIS A 204 HIS A 209 ASP A 360 3BY A 503 SITE 2 AC2 5 HOH A 786 SITE 1 AC3 11 ASN A 199 GLU A 201 CYS A 202 HIS A 204 SITE 2 AC3 11 CYS A 205 HIS A 209 THR A 356 ASP A 360 SITE 3 AC3 11 FE A 502 HOH A 786 HOH A 860 SITE 1 AC4 7 ARG A 14 ARG A 15 LEU A 16 GLU A 22 SITE 2 AC4 7 HOH A 787 HOH A 823 HOH A 831 SITE 1 AC5 5 THR A 61 LEU A 62 ARG A 63 GLU A 68 SITE 2 AC5 5 LYS A 95 SITE 1 AC6 5 LEU A 12 ASP A 13 ARG A 15 HOH A 821 SITE 2 AC6 5 HOH A 822 CRYST1 97.746 97.746 177.984 90.00 90.00 120.00 P 63 2 2 12 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 0.010231 0.005907 0.000000 0.00000 SCALE2 0.000000 0.011813 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005618 0.00000