HEADER OXIDOREDUCTASE 31-OCT-13 3WKU 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: SPHINGOBIUM; SOURCE 3 ORGANISM_TAXID: 627192; 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) KEYWDS TYPE II EXTRADIOL DIOXYGENASE, DOMAIN-SWAP DIMER, EXTRADIOL KEYWDS 2 DIOXYGENASE, FE2+ BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.SUGIMOTO,M.SENDA,D.KASAI,M.FUKUDA,E.MASAI,T.SENDA REVDAT 3 20-MAR-24 3WKU 1 REMARK LINK REVDAT 2 14-FEB-18 3WKU 1 REMARK REVDAT 1 30-APR-14 3WKU 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. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20862 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) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.314 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1098 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1520 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.3730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6449 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.04000 REMARK 3 B22 (A**2) : 2.36000 REMARK 3 B33 (A**2) : -1.25000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.22000 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): 0.481 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.397 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.891 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.923 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.859 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6650 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9020 ; 1.319 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 809 ; 6.389 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 327 ;34.859 ;23.394 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1053 ;18.771 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;17.178 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 932 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5220 ; 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): 4037 ; 0.533 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6470 ; 0.991 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2613 ; 1.220 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2550 ; 2.035 ; 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 3WKU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1000096461. 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 : 42572 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 56.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.03090 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 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: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.38250 REMARK 290 SMTRY3 2 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: 10130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 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 ALA A 22 REMARK 465 ASN A 23 REMARK 465 LYS A 24 REMARK 465 TYR A 25 REMARK 465 ASP A 26 REMARK 465 VAL A 414 REMARK 465 ALA A 415 REMARK 465 GLY A 416 REMARK 465 LYS A 417 REMARK 465 GLN A 418 REMARK 465 MET B 1 REMARK 465 ASN B 407 REMARK 465 ALA B 408 REMARK 465 ALA B 409 REMARK 465 ILE B 410 REMARK 465 THR B 411 REMARK 465 TYR B 412 REMARK 465 SER B 413 REMARK 465 VAL B 414 REMARK 465 ALA B 415 REMARK 465 GLY B 416 REMARK 465 LYS B 417 REMARK 465 GLN B 418 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 NH2 ARG A 171 OD1 ASP A 287 2.15 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 VAL A 10 132.10 177.62 REMARK 500 ALA A 17 -79.18 -74.28 REMARK 500 PHE A 18 14.22 -49.73 REMARK 500 ALA A 19 -61.24 -147.36 REMARK 500 PRO A 32 35.46 -87.25 REMARK 500 LYS A 48 86.67 50.62 REMARK 500 HIS A 59 66.67 -107.29 REMARK 500 PHE A 64 -86.34 -125.36 REMARK 500 ASP A 89 81.20 -56.98 REMARK 500 ALA A 126 -79.59 -109.60 REMARK 500 GLU A 137 -80.86 -68.89 REMARK 500 LEU A 190 -158.40 -89.59 REMARK 500 ASN A 203 77.45 -158.68 REMARK 500 ALA A 215 -70.59 -75.51 REMARK 500 ASP A 217 83.32 -152.10 REMARK 500 LEU A 222 60.00 -66.97 REMARK 500 ALA A 230 -74.26 -69.71 REMARK 500 GLU A 239 1.46 -58.63 REMARK 500 THR A 256 79.37 -49.15 REMARK 500 LEU A 257 3.94 -57.94 REMARK 500 HIS A 258 130.03 166.88 REMARK 500 TYR A 261 128.16 -172.16 REMARK 500 PHE A 262 -155.36 -137.14 REMARK 500 LEU A 263 78.73 -172.75 REMARK 500 PRO A 264 -79.29 -68.16 REMARK 500 SER A 265 -105.43 -98.80 REMARK 500 GLN A 277 -83.14 -103.41 REMARK 500 ALA A 280 5.32 -69.19 REMARK 500 ALA A 281 147.83 -179.36 REMARK 500 ILE A 304 107.86 -53.46 REMARK 500 SER A 348 -179.79 -62.62 REMARK 500 ASN A 407 -47.33 104.28 REMARK 500 ALA A 409 79.18 -112.50 REMARK 500 ASN B 23 53.62 37.27 REMARK 500 PRO B 28 -38.60 -29.64 REMARK 500 HIS B 59 63.78 -107.66 REMARK 500 THR B 61 -77.50 -114.01 REMARK 500 PHE B 64 -67.29 -134.51 REMARK 500 LEU B 114 -160.41 -124.94 REMARK 500 GLU B 137 16.59 -67.91 REMARK 500 HIS B 138 -11.75 -178.87 REMARK 500 PRO B 177 69.17 -100.51 REMARK 500 LEU B 190 -120.53 -84.65 REMARK 500 HIS B 192 145.02 -173.51 REMARK 500 ASN B 203 90.51 -163.53 REMARK 500 ASP B 217 53.77 -155.05 REMARK 500 VAL B 240 -15.45 -49.00 REMARK 500 SER B 265 -104.86 -131.14 REMARK 500 ASP B 279 66.49 -69.97 REMARK 500 ALA B 294 -71.00 -88.98 REMARK 500 REMARK 500 THIS ENTRY HAS 58 RAMACHANDRAN OUTLIERS. 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 GLU B 137 HIS B 138 146.24 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 FE A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 12 NE2 REMARK 620 2 HIS A 59 NE2 90.6 REMARK 620 3 GLU A 239 OE1 72.3 123.0 REMARK 620 4 GLU A 239 OE2 78.0 168.2 50.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GDE A 502 OAE REMARK 620 2 GDE A 502 OAD 60.0 REMARK 620 3 HIS B 12 NE2 128.3 115.6 REMARK 620 4 HIS B 59 NE2 72.0 131.3 87.0 REMARK 620 5 GLU B 239 OE1 151.1 127.9 76.6 98.0 REMARK 620 6 GLU B 239 OE2 137.6 81.8 82.8 146.1 48.2 REMARK 620 7 HOH B 601 O 72.6 71.3 159.1 103.0 83.8 78.7 REMARK 620 8 HOH B 602 O 101.3 134.1 108.6 60.6 51.8 92.3 62.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 12 NE2 REMARK 620 2 ASN B 57 OD1 87.1 REMARK 620 3 HIS B 59 NE2 102.4 100.6 REMARK 620 4 GLU B 239 OE1 108.0 96.1 145.9 REMARK 620 5 HOH B 602 O 165.5 107.1 73.2 73.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDE A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VJU RELATED DB: PDB REMARK 900 THE SAME PROTEIN (SUBSTRATE FREE). REMARK 900 RELATED ID: 3VJV RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEX WITH GALLATE (SPACE GROUP: C222(1)). REMARK 900 RELATED ID: 3VJW RELATED DB: PDB REMARK 900 THE SAME PROTEIN EXPOSED TO AEROBIC ATMOSPHERE. REMARK 900 RELATED ID: 3VJX RELATED DB: PDB REMARK 900 H124F DESB-GALLATE COMPLEX REMARK 900 RELATED ID: 3VJY RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEX WITH PCA. DBREF 3WKU A 1 418 UNP G2IKE5 G2IKE5_9SPHN 1 418 DBREF 3WKU B 1 418 UNP G2IKE5 G2IKE5_9SPHN 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 FE A 501 1 HET GDE A 502 12 HET FE B 501 2 HETNAM FE FE (III) ION HETNAM GDE 3,4,5-TRIHYDROXYBENZOIC ACID HETSYN GDE GALLATE FORMUL 3 FE 2(FE 3+) FORMUL 4 GDE C7 H6 O5 FORMUL 6 HOH *2(H2 O) HELIX 1 1 ILE A 33 LEU A 44 1 12 HELIX 2 2 ASP A 96 ASP A 110 1 15 HELIX 3 3 ASP A 123 VAL A 132 1 10 HELIX 4 4 LYS A 158 TYR A 176 1 19 HELIX 5 5 ASN A 203 ASP A 217 1 15 HELIX 6 6 VAL A 226 GLY A 234 1 9 HELIX 7 7 TRP A 235 GLU A 239 5 5 HELIX 8 8 VAL A 240 LEU A 250 1 11 HELIX 9 9 SER A 286 ALA A 294 1 9 HELIX 10 10 THR A 311 GLY A 318 1 8 HELIX 11 11 GLY A 318 ARG A 327 1 10 HELIX 12 12 LEU A 328 GLU A 330 5 3 HELIX 13 13 ASP A 332 ASP A 340 1 9 HELIX 14 14 ASP A 340 SER A 348 1 9 HELIX 15 15 THR A 351 ARG A 361 1 11 HELIX 16 16 ASP A 362 GLY A 370 1 9 HELIX 17 17 ILE A 372 LEU A 383 1 12 HELIX 18 18 GLY A 386 ARG A 395 1 10 HELIX 19 19 SER A 398 GLN A 403 1 6 HELIX 20 20 LYS A 404 ARG A 406 5 3 HELIX 21 21 THR B 13 ALA B 22 1 10 HELIX 22 22 TRP B 30 GLY B 36 1 7 HELIX 23 23 PHE B 37 LYS B 48 1 12 HELIX 24 24 ASP B 96 ASP B 110 1 15 HELIX 25 25 ASP B 123 LEU B 134 1 12 HELIX 26 26 LYS B 158 SER B 175 1 18 HELIX 27 27 ASN B 203 ASP B 217 1 15 HELIX 28 28 PRO B 218 LEU B 222 5 5 HELIX 29 29 THR B 225 GLY B 234 1 10 HELIX 30 30 TRP B 235 GLU B 239 5 5 HELIX 31 31 VAL B 240 ALA B 249 1 10 HELIX 32 32 SER B 286 ARG B 296 1 11 HELIX 33 33 GLU B 297 ALA B 299 5 3 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 ASN B 360 1 10 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 ARG B 395 1 10 HELIX 43 43 SER B 398 GLN B 403 1 6 SHEET 1 A 5 ARG A 143 ILE A 144 0 SHEET 2 A 5 VAL A 51 TYR A 56 1 N THR A 52 O ARG A 143 SHEET 3 A 5 LYS A 181 GLY A 186 1 O ALA A 183 N PHE A 53 SHEET 4 A 5 LYS A 3 ALA A 9 1 N PHE A 8 O GLY A 186 SHEET 5 A 5 PHE A 274 GLU A 275 -1 O PHE A 274 N GLY A 7 SHEET 1 B 6 ARG A 143 ILE A 144 0 SHEET 2 B 6 VAL A 51 TYR A 56 1 N THR A 52 O ARG A 143 SHEET 3 B 6 LEU A 147 CYS A 149 1 O LEU A 147 N TYR A 54 SHEET 4 B 6 PHE A 70 GLY A 73 -1 N ALA A 71 O GLN A 148 SHEET 5 B 6 ALA A 115 TRP A 117 1 O ALA A 115 N LEU A 72 SHEET 6 B 6 HIS B 66 SER B 68 -1 O TYR B 67 N TYR A 116 SHEET 1 C 9 HIS A 66 SER A 68 0 SHEET 2 C 9 ALA B 115 TRP B 117 -1 O TYR B 116 N TYR A 67 SHEET 3 C 9 PHE B 70 GLY B 73 1 N LEU B 72 O ALA B 115 SHEET 4 C 9 ARG B 143 CYS B 149 -1 O PRO B 146 N GLY B 73 SHEET 5 C 9 VAL B 51 TYR B 56 1 N THR B 52 O ARG B 143 SHEET 6 C 9 LYS B 181 THR B 187 1 O ALA B 185 N VAL B 55 SHEET 7 C 9 LYS B 3 VAL B 10 1 N LYS B 3 O VAL B 182 SHEET 8 C 9 ILE B 269 ASP B 276 -1 O PHE B 274 N GLY B 7 SHEET 9 C 9 VAL B 254 PHE B 262 -1 N PHE B 262 O ILE B 269 SHEET 1 D 2 GLU A 77 TYR A 78 0 SHEET 2 D 2 ILE A 93 LYS A 94 -1 O ILE A 93 N TYR A 78 SHEET 1 E 2 TYR A 261 PHE A 262 0 SHEET 2 E 2 ILE A 269 ALA A 270 -1 O ILE A 269 N PHE A 262 SHEET 1 F 2 GLU B 77 TYR B 78 0 SHEET 2 F 2 ILE B 93 LYS B 94 -1 O ILE B 93 N TYR B 78 LINK NE2 HIS A 12 FE FE A 501 1555 1555 2.49 LINK NE2 HIS A 59 FE FE A 501 1555 1555 2.15 LINK OE1 GLU A 239 FE FE A 501 1555 1555 2.34 LINK OE2 GLU A 239 FE FE A 501 1555 1555 2.71 LINK OAE GDE A 502 FE B FE B 501 1555 1555 2.43 LINK OAD GDE A 502 FE B FE B 501 1555 1555 2.79 LINK NE2 HIS B 12 FE A FE B 501 1555 1555 2.19 LINK NE2 HIS B 12 FE B FE B 501 1555 1555 2.56 LINK OD1 ASN B 57 FE A FE B 501 1555 1555 1.85 LINK NE2 HIS B 59 FE A FE B 501 1555 1555 2.21 LINK NE2 HIS B 59 FE B FE B 501 1555 1555 2.41 LINK OE1 GLU B 239 FE A FE B 501 1555 1555 1.79 LINK OE1 GLU B 239 FE B FE B 501 1555 1555 2.65 LINK OE2 GLU B 239 FE B FE B 501 1555 1555 2.66 LINK FE B FE B 501 O HOH B 601 1555 1555 1.96 LINK FE A FE B 501 O HOH B 602 1555 1555 2.01 LINK FE B FE B 501 O HOH B 602 1555 1555 2.57 CISPEP 1 HIS A 154 PRO A 155 0 10.34 CISPEP 2 GLY A 189 LEU A 190 0 -3.94 CISPEP 3 HIS B 154 PRO B 155 0 11.85 CISPEP 4 GLY B 189 LEU B 190 0 2.34 SITE 1 AC1 4 HIS A 12 ASN A 57 HIS A 59 GLU A 239 SITE 1 AC2 14 PHE A 374 GLU A 377 TYR A 391 TYR A 412 SITE 2 AC2 14 THR B 13 PRO B 14 HIS B 59 HIS B 124 SITE 3 AC2 14 HIS B 192 VAL B 194 GLU B 239 THR B 267 SITE 4 AC2 14 FE B 501 HOH B 601 SITE 1 AC3 7 GDE A 502 HIS B 12 ASN B 57 HIS B 59 SITE 2 AC3 7 GLU B 239 HOH B 601 HOH B 602 CRYST1 57.435 60.765 117.986 90.00 98.58 90.00 P 1 21 1 4 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 0.017411 0.000000 0.002626 0.00000 SCALE2 0.000000 0.016457 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008571 0.00000