HEADER OXIDOREDUCTASE 14-JAN-14 3WPM TITLE CRYSTAL STRUCTURE OF THE ANAEROBIC DESB-GALLATE COMPLEX BY CO- TITLE 2 CRYSTALLIZATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALLATE DIOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.13.11.-; COMPND 5 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); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID 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 2 08-NOV-23 3WPM 1 REMARK LINK REVDAT 1 30-APR-14 3WPM 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. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 29187 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1467 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.8993 - 6.8888 0.99 2638 138 0.1556 0.1731 REMARK 3 2 6.8888 - 5.4712 1.00 2643 141 0.1976 0.2595 REMARK 3 3 5.4712 - 4.7806 1.00 2634 141 0.1780 0.2176 REMARK 3 4 4.7806 - 4.3439 1.00 2629 140 0.1751 0.2153 REMARK 3 5 4.3439 - 4.0328 1.00 2658 141 0.1940 0.2706 REMARK 3 6 4.0328 - 3.7952 1.00 2595 138 0.2165 0.3170 REMARK 3 7 3.7952 - 3.6052 1.00 2658 140 0.2293 0.2925 REMARK 3 8 3.6052 - 3.4483 1.00 2639 137 0.2532 0.2863 REMARK 3 9 3.4483 - 3.3156 1.00 2674 144 0.2537 0.3639 REMARK 3 10 3.3156 - 3.2012 1.00 2576 131 0.2643 0.4080 REMARK 3 11 3.2012 - 3.1012 1.00 2667 140 0.2670 0.3547 REMARK 3 12 3.1012 - 3.0125 1.00 2680 143 0.2640 0.3217 REMARK 3 13 3.0125 - 2.9333 1.00 2618 140 0.2618 0.3343 REMARK 3 14 2.9333 - 2.8617 1.00 2647 143 0.2793 0.3936 REMARK 3 15 2.8617 - 2.7967 1.00 2589 133 0.2948 0.4450 REMARK 3 16 2.7967 - 2.7372 1.00 2734 146 0.2857 0.4642 REMARK 3 17 2.7372 - 2.6824 1.00 2605 137 0.2754 0.3873 REMARK 3 18 2.6824 - 2.6318 1.00 2591 139 0.2782 0.3866 REMARK 3 19 2.6318 - 2.5848 1.00 2707 143 0.2907 0.4120 REMARK 3 20 2.5848 - 2.5410 1.00 2596 135 0.3014 0.2924 REMARK 3 21 2.5410 - 2.5000 1.00 2663 143 0.3262 0.3970 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 6482 REMARK 3 ANGLE : 1.235 8817 REMARK 3 CHIRALITY : 0.080 929 REMARK 3 PLANARITY : 0.006 1165 REMARK 3 DIHEDRAL : 14.722 2294 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3WPM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000096633. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-12 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-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 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 : 29197 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 56.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 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) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 3WKU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 26% PEG8000, 0.1M SODIUM ACETATE, 0.1M REMARK 280 HEPES-NAOH, PH 7.75, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K 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 32.09250 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: 9880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 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 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 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 PHE A 37 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A 42 CG CD OE1 NE2 REMARK 470 GLU A 46 CG CD OE1 OE2 REMARK 470 LYS A 48 CG CD CE NZ REMARK 470 GLN A 87 CG CD OE1 NE2 REMARK 470 PHE A 127 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 137 CG CD OE1 OE2 REMARK 470 ARG A 160 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 171 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 GLU A 197 CG CD OE1 OE2 REMARK 470 ARG A 213 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 216 CG OD1 ND2 REMARK 470 GLU A 219 CG CD OE1 OE2 REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 LYS A 232 CG CD CE NZ REMARK 470 LEU A 245 CG CD1 CD2 REMARK 470 GLU A 253 CG CD OE1 OE2 REMARK 470 LYS A 255 CG CD CE NZ REMARK 470 THR A 256 OG1 CG2 REMARK 470 GLN A 259 CG CD OE1 NE2 REMARK 470 PHE A 262 CG CD1 CD2 CE1 CE2 CZ REMARK 470 MET A 266 CG SD CE REMARK 470 LEU A 273 CG CD1 CD2 REMARK 470 ASP A 279 CG OD1 OD2 REMARK 470 GLU A 288 CG CD OE1 OE2 REMARK 470 GLU B 76 CG CD OE1 OE2 REMARK 470 LYS B 94 CG CD CE NZ REMARK 470 HIS B 138 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 295 CG CD CE NZ REMARK 470 PHE B 333 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 335 CG CD CE NZ REMARK 470 ARG B 336 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 342 CG CD OE1 OE2 REMARK 470 TRP B 363 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 363 CZ3 CH2 REMARK 470 ILE B 388 CG1 CG2 CD1 REMARK 470 VAL B 390 CG1 CG2 REMARK 470 GLN B 403 CG CD OE1 NE2 REMARK 470 LYS B 404 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 PRO B 28 C - N - CA ANGL. DEV. = 9.5 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 17 -29.32 -167.94 REMARK 500 ALA A 19 -118.58 -117.91 REMARK 500 HIS A 20 -79.96 28.65 REMARK 500 LYS A 48 79.69 52.62 REMARK 500 PHE A 53 99.85 -67.15 REMARK 500 HIS A 59 52.07 -96.09 REMARK 500 MET A 60 32.03 70.23 REMARK 500 THR A 61 -72.02 -94.47 REMARK 500 PHE A 64 -83.28 -154.48 REMARK 500 ASP A 89 82.96 -42.64 REMARK 500 SER A 131 34.59 -76.67 REMARK 500 VAL A 132 -43.35 -146.60 REMARK 500 GLU A 137 -74.76 -55.74 REMARK 500 ASP A 179 87.40 -69.18 REMARK 500 LEU A 190 -153.69 -85.18 REMARK 500 SER A 191 127.26 -39.13 REMARK 500 ASN A 203 82.15 -167.20 REMARK 500 ALA A 238 1.61 -69.74 REMARK 500 VAL A 240 -8.19 -57.59 REMARK 500 VAL A 254 -160.67 -116.54 REMARK 500 THR A 256 85.78 -57.28 REMARK 500 TYR A 261 117.60 -165.65 REMARK 500 PRO A 264 -71.95 -70.24 REMARK 500 SER A 265 -112.86 -107.57 REMARK 500 THR A 271 131.26 -178.66 REMARK 500 GLN A 277 -101.63 -95.95 REMARK 500 ALA A 281 -172.12 60.03 REMARK 500 LYS B 24 40.56 -106.94 REMARK 500 HIS B 59 72.10 -105.95 REMARK 500 MET B 60 42.87 38.13 REMARK 500 THR B 61 -72.79 -104.54 REMARK 500 PHE B 64 -71.19 -154.99 REMARK 500 HIS B 69 -71.24 -76.61 REMARK 500 ASP B 96 79.83 -154.52 REMARK 500 LEU B 114 -166.95 -111.27 REMARK 500 ALA B 126 -62.37 -93.83 REMARK 500 HIS B 136 12.18 -156.84 REMARK 500 GLU B 137 35.02 -73.74 REMARK 500 HIS B 138 -90.31 -160.78 REMARK 500 LEU B 190 -126.69 -84.63 REMARK 500 HIS B 192 146.77 174.90 REMARK 500 ASN B 203 80.07 -154.40 REMARK 500 ASP B 217 58.36 -149.33 REMARK 500 VAL B 240 -9.58 -57.87 REMARK 500 SER B 265 -119.61 -133.15 REMARK 500 ALA B 281 128.69 -175.45 REMARK 500 ARG B 296 -52.94 -28.43 REMARK 500 VAL B 301 -29.97 -25.68 REMARK 500 GLU B 303 46.95 -79.95 REMARK 500 ARG B 336 -6.05 -153.60 REMARK 500 REMARK 500 THIS ENTRY HAS 56 RAMACHANDRAN OUTLIERS. 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 ASN A 57 OD1 REMARK 620 2 HIS A 59 NE2 94.0 REMARK 620 3 GLU A 239 OE1 77.4 144.2 REMARK 620 4 GLU A 239 OE2 104.7 158.5 53.0 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 HIS B 12 NE2 REMARK 620 2 ASN B 57 OD1 89.1 REMARK 620 3 HIS B 59 NE2 97.4 101.3 REMARK 620 4 GLU B 239 OE1 91.4 78.3 171.2 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 GLU B 239 OE2 REMARK 620 2 GDE B 502 OAD 105.9 REMARK 620 3 GDE B 502 OAE 167.3 61.6 REMARK 620 4 HOH B 601 O 112.6 80.7 64.6 REMARK 620 N 1 2 3 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 FE B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDE B 502 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 COMPLEXED WITH GALLATE (DIFFERENT SPACE GROUP: REMARK 900 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 COMPLEXED WITH PCA REMARK 900 RELATED ID: 3WKU RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEX WITH GALLATE (SOAKING METHOD) DBREF 3WPM A 1 418 UNP G2IKE5 G2IKE5_9SPHN 1 418 DBREF 3WPM 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 FE B 501 2 HET GDE B 502 12 HETNAM FE FE (III) ION HETNAM GDE 3,4,5-TRIHYDROXYBENZOIC ACID HETSYN GDE GALLATE FORMUL 3 FE 2(FE 3+) FORMUL 5 GDE C7 H6 O5 FORMUL 6 HOH *(H2 O) HELIX 1 1 THR A 13 ALA A 17 5 5 HELIX 2 2 TRP A 30 LEU A 44 1 15 HELIX 3 3 ASP A 96 ASP A 110 1 15 HELIX 4 4 ALA A 126 LEU A 134 1 9 HELIX 5 5 LYS A 158 SER A 175 1 18 HELIX 6 6 ASN A 203 ASP A 217 1 15 HELIX 7 7 PRO A 218 LEU A 222 5 5 HELIX 8 8 THR A 225 LYS A 232 1 8 HELIX 9 9 TRP A 235 GLU A 239 5 5 HELIX 10 10 VAL A 240 ALA A 249 1 10 HELIX 11 11 GLU A 288 ARG A 296 1 9 HELIX 12 12 GLU A 297 ALA A 299 5 3 HELIX 13 13 GLY A 300 ILE A 304 5 5 HELIX 14 14 THR A 311 ARG A 327 1 17 HELIX 15 15 GLU A 330 ASP A 340 1 11 HELIX 16 16 ASP A 340 SER A 348 1 9 HELIX 17 17 THR A 351 ASN A 360 1 10 HELIX 18 18 ASP A 362 GLY A 370 1 9 HELIX 19 19 ILE A 372 GLY A 384 1 13 HELIX 20 20 GLY A 386 ARG A 395 1 10 HELIX 21 21 SER A 398 THR A 405 1 8 HELIX 22 22 THR B 13 ALA B 22 1 10 HELIX 23 23 VAL B 29 GLY B 36 1 8 HELIX 24 24 PHE B 37 LYS B 48 1 12 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 TYR B 176 1 19 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 GLY B 248 1 9 HELIX 33 33 SER B 286 ARG B 296 1 11 HELIX 34 34 GLU B 297 ALA B 299 5 3 HELIX 35 35 GLY B 300 ILE B 304 5 5 HELIX 36 36 THR B 311 ARG B 327 1 17 HELIX 37 37 GLU B 330 VAL B 338 1 9 HELIX 38 38 ASP B 340 GLU B 347 1 8 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 ALA B 381 1 10 HELIX 42 42 GLY B 386 PHE B 394 1 9 HELIX 43 43 SER B 398 LYS B 404 1 7 SHEET 1 A 8 GLU A 77 TYR A 78 0 SHEET 2 A 8 ILE A 93 GLY A 95 -1 O ILE A 93 N TYR A 78 SHEET 3 A 8 ARG A 143 CYS A 149 1 O ILE A 144 N LYS A 94 SHEET 4 A 8 VAL A 51 TYR A 56 1 N THR A 52 O ARG A 143 SHEET 5 A 8 LYS A 181 GLY A 186 1 O ALA A 185 N PHE A 53 SHEET 6 A 8 LYS A 3 VAL A 10 1 N LYS A 3 O VAL A 182 SHEET 7 A 8 ILE A 269 LEU A 273 -1 O MET A 272 N ALA A 9 SHEET 8 A 8 HIS A 258 PHE A 262 -1 N HIS A 258 O LEU A 273 SHEET 1 B 6 GLU A 77 TYR A 78 0 SHEET 2 B 6 ILE A 93 GLY A 95 -1 O ILE A 93 N TYR A 78 SHEET 3 B 6 ARG A 143 CYS A 149 1 O ILE A 144 N LYS A 94 SHEET 4 B 6 PHE A 70 GLY A 73 -1 N GLY A 73 O PRO A 146 SHEET 5 B 6 ALA A 115 TRP A 117 1 O TRP A 117 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 GLN B 148 N ALA B 71 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 PHE B 53 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 MET B 272 N ALA B 9 SHEET 9 C 9 VAL B 254 PHE B 262 -1 N PHE B 262 O ILE B 269 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 OD1 ASN A 57 FE FE A 501 1555 1555 2.73 LINK NE2 HIS A 59 FE FE A 501 1555 1555 2.28 LINK OE1 GLU A 239 FE FE A 501 1555 1555 2.06 LINK OE2 GLU A 239 FE FE A 501 1555 1555 2.69 LINK NE2 HIS B 12 FE A FE B 501 1555 1555 2.27 LINK OD1 ASN B 57 FE A FE B 501 1555 1555 2.23 LINK NE2 HIS B 59 FE A FE B 501 1555 1555 2.09 LINK OE1 GLU B 239 FE A FE B 501 1555 1555 1.95 LINK OE2 GLU B 239 FE B FE B 501 1555 1555 2.59 LINK FE B FE B 501 OAD GDE B 502 1555 1555 2.53 LINK FE B FE B 501 OAE GDE B 502 1555 1555 2.65 LINK FE B FE B 501 O HOH B 601 1555 1555 2.51 CISPEP 1 HIS A 154 PRO A 155 0 6.40 CISPEP 2 GLY A 189 LEU A 190 0 -3.77 CISPEP 3 HIS B 154 PRO B 155 0 9.22 CISPEP 4 GLY B 189 LEU B 190 0 -6.96 CISPEP 5 GLY B 384 ILE B 385 0 1.33 SITE 1 AC1 4 HIS A 12 ASN A 57 HIS A 59 GLU A 239 SITE 1 AC2 6 HIS B 12 ASN B 57 HIS B 59 GLU B 239 SITE 2 AC2 6 GDE B 502 HOH B 601 SITE 1 AC3 12 GLU A 377 TYR A 391 TYR A 412 THR B 13 SITE 2 AC3 12 PRO B 14 HIS B 59 HIS B 124 HIS B 192 SITE 3 AC3 12 MET B 266 THR B 267 FE B 501 HOH B 601 CRYST1 58.105 64.185 117.896 90.00 97.19 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 0.017210 0.000000 0.002170 0.00000 SCALE2 0.000000 0.015580 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008549 0.00000