HEADER OXIDOREDUCTASE 21-FEB-14 3WR9 TITLE CRYSTAL STRUCTURE OF THE ANAEROBIC DESB-GALLATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALLATE DIOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DESB, TYPE II EXTRADIOL DIOXYGENASE; COMPND 5 EC: 1.13.11.58; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPHINGOMONAS PAUCIMOBILIS; SOURCE 3 ORGANISM_TAXID: 13689; SOURCE 4 STRAIN: SYK-6; SOURCE 5 GENE: DESB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PEVK3G KEYWDS OXIDOREDUCTASE, EXTRADIOL DIOXYGENASE, FE2+ BINDING, DOMAIN-SWAP KEYWDS 2 DIMER EXPDTA X-RAY DIFFRACTION AUTHOR K.SUGIMOTO,M.SENDA,D.KASAI,M.FUKUDA,E.MASAI,T.SENDA REVDAT 4 03-APR-24 3WR9 1 REMARK REVDAT 3 20-MAR-24 3WR9 1 REMARK LINK REVDAT 2 14-FEB-18 3WR9 1 REMARK REVDAT 1 30-APR-14 3WR9 0 JRNL AUTH K.SUGIMOTO,M.SENDA,D.KASAI,M.FUKUDA,E.MASAI,T.SENDA JRNL TITL MOLECULAR MECHANISM OF STRICT SUBSTRATE SPECIFICITY OF AN JRNL TITL 2 EXTRADIOL DIOXYGENASE, DESB, DERIVED FROM SPHINGOBIUM SP. JRNL TITL 3 SYK-6 JRNL REF PLOS ONE V. 9 92249 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 24657997 JRNL DOI 10.1371/JOURNAL.PONE.0092249 REMARK 2 REMARK 2 RESOLUTION. 2.40 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 38540 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2029 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2819 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 149 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6585 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 1.64000 REMARK 3 B33 (A**2) : -1.60000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.245 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.165 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.046 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6800 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9225 ; 1.293 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 830 ; 5.850 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 331 ;34.889 ;23.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1075 ;13.710 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;18.069 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 954 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5338 ; 0.006 ; 0.021 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): 4136 ; 0.558 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6625 ; 1.102 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2664 ; 1.904 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2600 ; 3.184 ; 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 : 1.40 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 3WR9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000096692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A 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 : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40553 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 53.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.770 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.02 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.280 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: DESB SUBSTRATE-FREE FORM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG8000, 0.1M SODIUM ACETATE, 0.1M REMARK 280 HEPES-NAOH, PH 7.75, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 52.24900 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 52.24900 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 61.76150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 79.59100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 61.76150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 79.59100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 52.24900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 61.76150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 79.59100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 52.24900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 61.76150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 79.59100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 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 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 GLN A 418 REMARK 465 MET B 1 REMARK 465 GLN B 418 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 TYR B 25 CG CD1 CD2 CE1 CE2 CZ OH REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 137 FE FE2 A 502 3654 1.50 REMARK 500 NE2 HIS A 138 FE FE2 A 502 3654 1.93 REMARK 500 NE2 HIS B 138 FE FE2 B 502 4555 2.03 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 11 152.42 -44.72 REMARK 500 THR A 61 -65.27 -108.22 REMARK 500 PHE A 64 -72.52 -142.40 REMARK 500 GLU A 111 35.84 70.25 REMARK 500 ALA A 126 -63.65 -103.40 REMARK 500 LEU A 190 -123.36 -84.99 REMARK 500 ASP A 217 53.92 -151.12 REMARK 500 VAL A 240 -9.90 -59.15 REMARK 500 SER A 265 -110.10 -118.90 REMARK 500 THR B 13 137.78 -38.22 REMARK 500 THR B 61 -70.52 -106.43 REMARK 500 PHE B 64 -72.46 -143.42 REMARK 500 HIS B 138 -22.02 66.71 REMARK 500 PRO B 177 47.36 -83.30 REMARK 500 LEU B 190 -127.12 -79.01 REMARK 500 HIS B 192 150.87 179.28 REMARK 500 ASP B 217 55.22 -150.30 REMARK 500 SER B 265 -111.50 -134.66 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 FE2 A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 12 NE2 REMARK 620 2 ASN A 57 OD1 99.2 REMARK 620 3 HIS A 59 NE2 94.0 106.2 REMARK 620 4 GLU A 239 OE1 108.3 83.1 154.4 REMARK 620 5 HOH A 691 O 166.8 93.6 85.1 70.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 12 NE2 REMARK 620 2 HIS A 59 NE2 75.5 REMARK 620 3 GDE A 503 OAE 120.8 82.5 REMARK 620 4 GDE A 503 OAC 101.8 152.2 75.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 20 NE2 REMARK 620 2 HIS A 136 NE2 111.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 12 NE2 REMARK 620 2 HIS B 59 NE2 85.1 REMARK 620 3 GDE B 503 OAE 125.5 85.1 REMARK 620 4 GDE B 503 OAD 102.1 153.2 69.6 REMARK 620 5 HOH B 616 O 143.6 112.4 88.8 76.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 12 NE2 REMARK 620 2 ASN B 57 OD1 103.3 REMARK 620 3 HIS B 59 NE2 87.6 105.2 REMARK 620 4 GLU B 239 OE1 104.0 93.3 155.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 20 NE2 REMARK 620 2 HIS B 136 NE2 111.9 REMARK 620 3 HOH B 608 O 106.5 116.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDE A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE2 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDE B 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WKU RELATED DB: PDB REMARK 900 RELATED ID: 3WPM RELATED DB: PDB REMARK 900 RELATED ID: 3WR3 RELATED DB: PDB REMARK 900 RELATED ID: 3WR4 RELATED DB: PDB REMARK 900 RELATED ID: 3WR8 RELATED DB: PDB REMARK 900 RELATED ID: 3WRA RELATED DB: PDB REMARK 900 RELATED ID: 3WRB RELATED DB: PDB REMARK 900 RELATED ID: 3WRC RELATED DB: PDB DBREF 3WR9 A 1 418 UNP Q5NTE5 Q5NTE5_SPHPI 1 418 DBREF 3WR9 B 1 418 UNP Q5NTE5 Q5NTE5_SPHPI 1 418 SEQRES 1 A 418 MET ALA LYS ILE ILE GLY GLY PHE ALA VAL SER HIS THR SEQRES 2 A 418 PRO THR ILE ALA PHE ALA HIS ASP ALA ASN LYS TYR ASP SEQRES 3 A 418 ASP PRO VAL TRP ALA PRO ILE PHE GLN GLY PHE GLU PRO SEQRES 4 A 418 VAL LYS GLN TRP LEU ALA GLU GLN LYS PRO ASP VAL THR SEQRES 5 A 418 PHE TYR VAL TYR ASN ASP HIS MET THR SER PHE PHE GLU SEQRES 6 A 418 HIS TYR SER HIS PHE ALA LEU GLY VAL GLY GLU GLU TYR SEQRES 7 A 418 SER PRO ALA ASP GLU GLY GLY GLY GLN ARG ASP LEU PRO SEQRES 8 A 418 PRO ILE LYS GLY ASP PRO GLU LEU ALA LYS HIS ILE ALA SEQRES 9 A 418 GLU CYS LEU VAL ALA ASP GLU PHE ASP LEU ALA TYR TRP SEQRES 10 A 418 GLN GLY MET GLY LEU ASP HIS GLY ALA PHE SER PRO LEU SEQRES 11 A 418 SER VAL LEU LEU PRO HIS GLU HIS GLY TRP PRO CYS ARG SEQRES 12 A 418 ILE VAL PRO LEU GLN CYS GLY VAL LEU GLN HIS PRO ILE SEQRES 13 A 418 PRO LYS ALA ARG ARG PHE TRP ASN PHE GLY ARG SER LEU SEQRES 14 A 418 ARG ARG ALA ILE GLN SER TYR PRO ARG ASP ILE LYS VAL SEQRES 15 A 418 ALA ILE ALA GLY THR GLY GLY LEU SER HIS GLN VAL HIS SEQRES 16 A 418 GLY GLU ARG ALA GLY PHE ASN ASN THR GLU TRP ASP MET SEQRES 17 A 418 GLU PHE MET GLU ARG LEU ALA ASN ASP PRO GLU SER LEU SEQRES 18 A 418 LEU GLY ALA THR VAL THR ASP LEU ALA LYS LYS GLY GLY SEQRES 19 A 418 TRP GLU GLY ALA GLU VAL VAL MET TRP LEU LEU MET ARG SEQRES 20 A 418 GLY ALA LEU SER PRO GLU VAL LYS THR LEU HIS GLN SER SEQRES 21 A 418 TYR PHE LEU PRO SER MET THR ALA ILE ALA THR MET LEU SEQRES 22 A 418 PHE GLU ASP GLN GLY ASP ALA ALA PRO PRO ALA GLU SER SEQRES 23 A 418 ASP GLU ALA LEU ARG ALA ARG ALA LYS ARG GLU LEU ALA SEQRES 24 A 418 GLY VAL GLU GLU ILE GLU GLY THR TYR PRO PHE THR ILE SEQRES 25 A 418 ASP ARG ALA VAL LYS GLY PHE ARG ILE ASN HIS PHE LEU SEQRES 26 A 418 HIS ARG LEU ILE GLU PRO ASP PHE ARG LYS ARG PHE VAL SEQRES 27 A 418 GLU ASP PRO GLU GLY LEU PHE ALA GLU SER ASP LEU THR SEQRES 28 A 418 GLU GLU GLU LYS SER LEU ILE ARG ASN ARG ASP TRP ILE SEQRES 29 A 418 GLY MET ILE HIS TYR GLY VAL ILE PHE PHE MET LEU GLU SEQRES 30 A 418 LYS MET ALA ALA VAL LEU GLY ILE GLY ASN ILE ASP VAL SEQRES 31 A 418 TYR ALA ALA PHE ARG GLY LEU SER VAL PRO GLU PHE GLN SEQRES 32 A 418 LYS THR ARG ASN ALA ALA ILE THR TYR SER VAL ALA GLY SEQRES 33 A 418 LYS GLN SEQRES 1 B 418 MET ALA LYS ILE ILE GLY GLY PHE ALA VAL SER HIS THR SEQRES 2 B 418 PRO THR ILE ALA PHE ALA HIS ASP ALA ASN LYS TYR ASP SEQRES 3 B 418 ASP PRO VAL TRP ALA PRO ILE PHE GLN GLY PHE GLU PRO SEQRES 4 B 418 VAL LYS GLN TRP LEU ALA GLU GLN LYS PRO ASP VAL THR SEQRES 5 B 418 PHE TYR VAL TYR ASN ASP HIS MET THR SER PHE PHE GLU SEQRES 6 B 418 HIS TYR SER HIS PHE ALA LEU GLY VAL GLY GLU GLU TYR SEQRES 7 B 418 SER PRO ALA ASP GLU GLY GLY GLY GLN ARG ASP LEU PRO SEQRES 8 B 418 PRO ILE LYS GLY ASP PRO GLU LEU ALA LYS HIS ILE ALA SEQRES 9 B 418 GLU CYS LEU VAL ALA ASP GLU PHE ASP LEU ALA TYR TRP SEQRES 10 B 418 GLN GLY MET GLY LEU ASP HIS GLY ALA PHE SER PRO LEU SEQRES 11 B 418 SER VAL LEU LEU PRO HIS GLU HIS GLY TRP PRO CYS ARG SEQRES 12 B 418 ILE VAL PRO LEU GLN CYS GLY VAL LEU GLN HIS PRO ILE SEQRES 13 B 418 PRO LYS ALA ARG ARG PHE TRP ASN PHE GLY ARG SER LEU SEQRES 14 B 418 ARG ARG ALA ILE GLN SER TYR PRO ARG ASP ILE LYS VAL SEQRES 15 B 418 ALA ILE ALA GLY THR GLY GLY LEU SER HIS GLN VAL HIS SEQRES 16 B 418 GLY GLU ARG ALA GLY PHE ASN ASN THR GLU TRP ASP MET SEQRES 17 B 418 GLU PHE MET GLU ARG LEU ALA ASN ASP PRO GLU SER LEU SEQRES 18 B 418 LEU GLY ALA THR VAL THR ASP LEU ALA LYS LYS GLY GLY SEQRES 19 B 418 TRP GLU GLY ALA GLU VAL VAL MET TRP LEU LEU MET ARG SEQRES 20 B 418 GLY ALA LEU SER PRO GLU VAL LYS THR LEU HIS GLN SER SEQRES 21 B 418 TYR PHE LEU PRO SER MET THR ALA ILE ALA THR MET LEU SEQRES 22 B 418 PHE GLU ASP GLN GLY ASP ALA ALA PRO PRO ALA GLU SER SEQRES 23 B 418 ASP GLU ALA LEU ARG ALA ARG ALA LYS ARG GLU LEU ALA SEQRES 24 B 418 GLY VAL GLU GLU ILE GLU GLY THR TYR PRO PHE THR ILE SEQRES 25 B 418 ASP ARG ALA VAL LYS GLY PHE ARG ILE ASN HIS PHE LEU SEQRES 26 B 418 HIS ARG LEU ILE GLU PRO ASP PHE ARG LYS ARG PHE VAL SEQRES 27 B 418 GLU ASP PRO GLU GLY LEU PHE ALA GLU SER ASP LEU THR SEQRES 28 B 418 GLU GLU GLU LYS SER LEU ILE ARG ASN ARG ASP TRP ILE SEQRES 29 B 418 GLY MET ILE HIS TYR GLY VAL ILE PHE PHE MET LEU GLU SEQRES 30 B 418 LYS MET ALA ALA VAL LEU GLY ILE GLY ASN ILE ASP VAL SEQRES 31 B 418 TYR ALA ALA PHE ARG GLY LEU SER VAL PRO GLU PHE GLN SEQRES 32 B 418 LYS THR ARG ASN ALA ALA ILE THR TYR SER VAL ALA GLY SEQRES 33 B 418 LYS GLN HET FE2 A 501 2 HET FE2 A 502 1 HET GDE A 503 12 HET FE2 B 501 2 HET FE2 B 502 1 HET GDE B 503 12 HETNAM FE2 FE (II) ION HETNAM GDE 3,4,5-TRIHYDROXYBENZOIC ACID HETSYN GDE GALLATE FORMUL 3 FE2 4(FE 2+) FORMUL 5 GDE 2(C7 H6 O5) FORMUL 9 HOH *165(H2 O) HELIX 1 1 THR A 13 ALA A 22 1 10 HELIX 2 2 ASN A 23 ASP A 27 5 5 HELIX 3 3 TRP A 30 LYS A 48 1 19 HELIX 4 4 ASP A 96 ASP A 110 1 15 HELIX 5 5 ASP A 123 LEU A 134 1 12 HELIX 6 6 LYS A 158 SER A 175 1 18 HELIX 7 7 ASN A 203 ASP A 217 1 15 HELIX 8 8 PRO A 218 LEU A 222 5 5 HELIX 9 9 THR A 225 GLY A 234 1 10 HELIX 10 10 TRP A 235 GLU A 239 5 5 HELIX 11 11 VAL A 240 LEU A 250 1 11 HELIX 12 12 SER A 286 ARG A 296 1 11 HELIX 13 13 GLY A 300 ILE A 304 5 5 HELIX 14 14 THR A 311 GLY A 318 1 8 HELIX 15 15 GLY A 318 ARG A 327 1 10 HELIX 16 16 GLU A 330 ASP A 340 1 11 HELIX 17 17 ASP A 340 SER A 348 1 9 HELIX 18 18 THR A 351 ASN A 360 1 10 HELIX 19 19 ASP A 362 GLY A 370 1 9 HELIX 20 20 ILE A 372 LEU A 383 1 12 HELIX 21 21 GLY A 386 GLY A 396 1 11 HELIX 22 22 SER A 398 LYS A 404 1 7 HELIX 23 23 THR B 13 ALA B 22 1 10 HELIX 24 24 ALA B 31 LYS B 48 1 18 HELIX 25 25 ASP B 96 ASP B 110 1 15 HELIX 26 26 ASP B 123 LEU B 134 1 12 HELIX 27 27 LYS B 158 SER B 175 1 18 HELIX 28 28 ASN B 203 ASP B 217 1 15 HELIX 29 29 PRO B 218 LEU B 222 5 5 HELIX 30 30 THR B 225 GLY B 234 1 10 HELIX 31 31 TRP B 235 GLU B 239 5 5 HELIX 32 32 VAL B 240 ALA B 249 1 10 HELIX 33 33 SER B 286 LYS B 295 1 10 HELIX 34 34 GLY B 300 ILE B 304 5 5 HELIX 35 35 THR B 311 GLY B 318 1 8 HELIX 36 36 GLY B 318 ARG B 327 1 10 HELIX 37 37 GLU B 330 ASP B 340 1 11 HELIX 38 38 ASP B 340 SER B 348 1 9 HELIX 39 39 THR B 351 ARG B 361 1 11 HELIX 40 40 ASP B 362 GLY B 370 1 9 HELIX 41 41 ILE B 372 LEU B 383 1 12 HELIX 42 42 GLY B 386 GLY B 396 1 11 HELIX 43 43 SER B 398 LYS B 404 1 7 SHEET 1 A 9 LYS A 255 PHE A 262 0 SHEET 2 A 9 ILE A 269 GLU A 275 -1 O GLU A 275 N LYS A 255 SHEET 3 A 9 LYS A 3 VAL A 10 -1 N GLY A 7 O PHE A 274 SHEET 4 A 9 LYS A 181 THR A 187 1 O VAL A 182 N LYS A 3 SHEET 5 A 9 VAL A 51 TYR A 56 1 N PHE A 53 O ALA A 183 SHEET 6 A 9 ARG A 143 CYS A 149 1 O LEU A 147 N TYR A 54 SHEET 7 A 9 PHE A 70 GLY A 73 -1 N GLY A 73 O PRO A 146 SHEET 8 A 9 ALA A 115 TRP A 117 1 O ALA A 115 N LEU A 72 SHEET 9 A 9 HIS B 66 SER B 68 -1 O TYR B 67 N TYR A 116 SHEET 1 B 9 HIS A 66 SER A 68 0 SHEET 2 B 9 ALA B 115 TRP B 117 -1 O TYR B 116 N TYR A 67 SHEET 3 B 9 PHE B 70 GLY B 73 1 N LEU B 72 O ALA B 115 SHEET 4 B 9 ARG B 143 CYS B 149 -1 O PRO B 146 N GLY B 73 SHEET 5 B 9 VAL B 51 TYR B 56 1 N TYR B 54 O LEU B 147 SHEET 6 B 9 LYS B 181 THR B 187 1 O ALA B 185 N VAL B 55 SHEET 7 B 9 LYS B 3 VAL B 10 1 N LYS B 3 O VAL B 182 SHEET 8 B 9 ILE B 269 ASP B 276 -1 O PHE B 274 N GLY B 7 SHEET 9 B 9 VAL B 254 PHE B 262 -1 N PHE B 262 O ILE B 269 SHEET 1 C 2 GLU A 77 TYR A 78 0 SHEET 2 C 2 ILE A 93 LYS A 94 -1 O ILE A 93 N TYR A 78 SHEET 1 D 2 GLU B 77 TYR B 78 0 SHEET 2 D 2 ILE B 93 LYS B 94 -1 O ILE B 93 N TYR B 78 LINK NE2 HIS A 12 FE BFE2 A 501 1555 1555 2.10 LINK NE2 HIS A 12 FE AFE2 A 501 1555 1555 2.54 LINK NE2 HIS A 20 FE FE2 A 502 1555 1555 2.00 LINK OD1 ASN A 57 FE BFE2 A 501 1555 1555 2.30 LINK NE2 HIS A 59 FE BFE2 A 501 1555 1555 1.94 LINK NE2 HIS A 59 FE AFE2 A 501 1555 1555 2.27 LINK NE2 HIS A 136 FE FE2 A 502 1555 1555 2.04 LINK OE1 GLU A 239 FE BFE2 A 501 1555 1555 2.13 LINK FE AFE2 A 501 OAE GDE A 503 1555 1555 1.95 LINK FE AFE2 A 501 OAC GDE A 503 1555 1555 2.50 LINK FE BFE2 A 501 O HOH A 691 1555 1555 2.13 LINK NE2 HIS B 12 FE BFE2 B 501 1555 1555 2.01 LINK NE2 HIS B 12 FE AFE2 B 501 1555 1555 2.23 LINK NE2 HIS B 20 FE FE2 B 502 1555 1555 1.94 LINK OD1 ASN B 57 FE AFE2 B 501 1555 1555 2.45 LINK NE2 HIS B 59 FE AFE2 B 501 1555 1555 2.15 LINK NE2 HIS B 59 FE BFE2 B 501 1555 1555 2.45 LINK NE2 HIS B 136 FE FE2 B 502 1555 1555 1.88 LINK OE1 GLU B 239 FE AFE2 B 501 1555 1555 2.08 LINK FE BFE2 B 501 OAE GDE B 503 1555 1555 1.91 LINK FE BFE2 B 501 OAD GDE B 503 1555 1555 2.75 LINK FE BFE2 B 501 O HOH B 616 1555 1555 1.86 LINK FE FE2 B 502 O HOH B 608 1555 1555 2.31 CISPEP 1 HIS A 154 PRO A 155 0 5.72 CISPEP 2 GLY A 189 LEU A 190 0 -9.66 CISPEP 3 HIS B 154 PRO B 155 0 7.89 CISPEP 4 GLY B 189 LEU B 190 0 -5.14 SITE 1 AC1 6 HIS A 12 ASN A 57 HIS A 59 GLU A 239 SITE 2 AC1 6 GDE A 503 HOH A 691 SITE 1 AC2 4 HIS A 20 HIS A 136 GLU A 137 HIS A 138 SITE 1 AC3 14 HIS A 12 THR A 13 PRO A 14 HIS A 59 SITE 2 AC3 14 HIS A 124 HIS A 192 MET A 266 THR A 267 SITE 3 AC3 14 FE2 A 501 HOH A 610 PHE B 374 GLU B 377 SITE 4 AC3 14 TYR B 391 TYR B 412 SITE 1 AC4 6 HIS B 12 ASN B 57 HIS B 59 GLU B 239 SITE 2 AC4 6 GDE B 503 HOH B 616 SITE 1 AC5 4 HIS B 20 HIS B 136 HIS B 138 HOH B 608 SITE 1 AC6 16 PHE A 374 GLU A 377 TYR A 391 TYR A 412 SITE 2 AC6 16 HIS B 12 THR B 13 PRO B 14 HIS B 59 SITE 3 AC6 16 HIS B 124 HIS B 192 MET B 266 THR B 267 SITE 4 AC6 16 FE2 B 501 HOH B 612 HOH B 616 HOH B 626 CRYST1 123.523 159.182 104.498 90.00 90.00 90.00 C 2 2 21 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 0.008096 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006282 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009570 0.00000