HEADER OXIDOREDUCTASE 13-FEB-14 3WR3 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 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) 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 08-NOV-23 3WR3 1 REMARK LINK REVDAT 2 14-FEB-18 3WR3 1 REMARK REVDAT 1 30-APR-14 3WR3 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: DEV_1539) 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) : 19.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 3 NUMBER OF REFLECTIONS : 28045 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1402 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 19.6955 - 6.5912 0.91 2668 138 0.1694 0.2413 REMARK 3 2 6.5912 - 5.2645 0.96 2821 148 0.1991 0.2449 REMARK 3 3 5.2645 - 4.6088 0.95 2792 146 0.1821 0.2380 REMARK 3 4 4.6088 - 4.1918 0.94 2771 148 0.1851 0.2366 REMARK 3 5 4.1918 - 3.8938 0.91 2647 145 0.2192 0.3412 REMARK 3 6 3.8938 - 3.6658 0.94 2784 149 0.2298 0.3085 REMARK 3 7 3.6658 - 3.4833 0.93 2714 143 0.2433 0.3324 REMARK 3 8 3.4833 - 3.3324 0.95 2810 147 0.2455 0.3374 REMARK 3 9 3.3324 - 3.2047 0.96 2743 149 0.2676 0.3602 REMARK 3 10 3.2047 - 3.0945 0.93 2772 143 0.2898 0.3883 REMARK 3 11 3.0945 - 2.9981 0.89 2620 137 0.3071 0.4883 REMARK 3 12 2.9981 - 2.9127 0.85 2486 131 0.3177 0.4110 REMARK 3 13 2.9127 - 2.8362 0.85 2581 135 0.3063 0.4027 REMARK 3 14 2.8362 - 2.7672 0.86 2481 131 0.2894 0.3667 REMARK 3 15 2.7672 - 2.7045 0.88 2593 136 0.2794 0.4125 REMARK 3 16 2.7045 - 2.6471 0.92 2706 143 0.3153 0.4451 REMARK 3 17 2.6471 - 2.5942 0.89 2647 138 0.2998 0.3873 REMARK 3 18 2.5942 - 2.5454 0.88 2517 127 0.2964 0.3443 REMARK 3 19 2.5454 - 2.5000 0.90 2728 146 0.2964 0.4326 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) : 38.570 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 6650 REMARK 3 ANGLE : 1.335 9020 REMARK 3 CHIRALITY : 0.052 932 REMARK 3 PLANARITY : 0.008 1188 REMARK 3 DIHEDRAL : 15.916 2408 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 3WR3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000096686. 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 : 68790 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 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 (%): 47.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 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 32.01000 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: 10040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 42 CA CD REMARK 480 ASP A 228 CG REMARK 480 GLU A 253 CD 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 O ARG A 160 ND2 ASN A 164 2.09 REMARK 500 NH2 ARG A 170 OD1 ASP A 279 2.15 REMARK 500 NH2 ARG A 171 O GLU A 285 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 263 CA - CB - CG ANGL. DEV. = 15.7 DEGREES REMARK 500 PRO B 28 C - N - CA ANGL. DEV. = 10.0 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 HIS A 20 -57.33 -25.45 REMARK 500 PRO A 28 -18.42 -49.11 REMARK 500 GLU A 38 44.55 -95.02 REMARK 500 VAL A 40 17.89 -164.77 REMARK 500 GLN A 42 -73.58 -21.47 REMARK 500 LYS A 48 80.58 40.46 REMARK 500 TYR A 56 -159.56 -137.39 REMARK 500 HIS A 59 58.36 -90.65 REMARK 500 PHE A 64 -78.72 -145.54 REMARK 500 ASP A 89 98.60 -60.11 REMARK 500 ASP A 123 -159.54 -99.32 REMARK 500 SER A 131 17.20 -60.23 REMARK 500 PRO A 135 96.83 -56.72 REMARK 500 LEU A 190 -116.92 -109.39 REMARK 500 ALA A 199 91.85 -61.80 REMARK 500 ASN A 203 101.44 -161.72 REMARK 500 ASP A 217 63.49 -154.71 REMARK 500 VAL A 240 16.16 -68.03 REMARK 500 THR A 256 101.73 -49.06 REMARK 500 GLN A 259 55.70 -164.71 REMARK 500 TYR A 261 129.33 -174.20 REMARK 500 PRO A 264 -135.21 -79.72 REMARK 500 SER A 265 -90.85 -46.69 REMARK 500 THR A 271 111.38 -170.53 REMARK 500 ALA A 281 165.98 149.96 REMARK 500 SER A 348 -173.84 -62.46 REMARK 500 THR A 351 177.62 -55.18 REMARK 500 ASN B 23 64.30 60.10 REMARK 500 HIS B 59 72.19 -110.32 REMARK 500 THR B 61 -83.00 -100.19 REMARK 500 PHE B 64 -79.35 -130.24 REMARK 500 HIS B 69 -76.31 -78.36 REMARK 500 HIS B 136 33.06 -160.41 REMARK 500 GLU B 137 92.14 -69.92 REMARK 500 HIS B 138 81.86 47.59 REMARK 500 PRO B 177 53.19 -65.00 REMARK 500 LEU B 190 -127.66 -83.39 REMARK 500 HIS B 192 146.58 173.87 REMARK 500 ASP B 217 69.71 -162.47 REMARK 500 SER B 265 -122.79 -136.08 REMARK 500 ALA B 268 95.99 -65.36 REMARK 500 ALA B 281 134.60 -179.43 REMARK 500 ARG B 296 -52.15 -8.98 REMARK 500 LYS B 404 96.47 -58.30 REMARK 500 THR B 405 -77.69 -138.20 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 A 38 PRO A 39 146.64 REMARK 500 VAL A 40 LYS A 41 145.28 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 ND2 103.8 REMARK 620 3 HIS A 59 NE2 90.1 73.0 REMARK 620 4 GLU A 239 OE1 97.3 104.7 172.6 REMARK 620 N 1 2 3 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 ND2 108.6 REMARK 620 3 HIS B 59 NE2 97.0 81.4 REMARK 620 4 GLU B 239 OE1 84.0 93.0 174.4 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 FE2 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 FE2 B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VJU RELATED DB: PDB REMARK 900 RELATED ID: 3VJV RELATED DB: PDB REMARK 900 RELATED ID: 3VJW RELATED DB: PDB REMARK 900 RELATED ID: 3VJX RELATED DB: PDB REMARK 900 RELATED ID: 3VJY RELATED DB: PDB REMARK 900 RELATED ID: 3WKU RELATED DB: PDB REMARK 900 RELATED ID: 3WR4 RELATED DB: PDB DBREF 3WR3 A 1 418 UNP G2IKE5 G2IKE5_9SPHN 1 418 DBREF 3WR3 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 FE2 A 501 1 HET GDE A 502 12 HET FE2 B 501 1 HETNAM FE2 FE (II) ION HETNAM GDE 3,4,5-TRIHYDROXYBENZOIC ACID HETSYN GDE GALLATE FORMUL 3 FE2 2(FE 2+) FORMUL 4 GDE C7 H6 O5 HELIX 1 1 PRO A 14 ALA A 19 1 6 HELIX 2 2 TRP A 30 GLN A 35 1 6 HELIX 3 3 VAL A 40 GLN A 47 1 8 HELIX 4 4 ASP A 96 ASP A 110 1 15 HELIX 5 5 ALA A 126 LEU A 134 1 9 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 ARG A 247 1 8 HELIX 12 12 GLY A 248 LEU A 250 5 3 HELIX 13 13 SER A 286 ARG A 296 1 11 HELIX 14 14 GLU A 297 ALA A 299 5 3 HELIX 15 15 GLY A 300 ILE A 304 5 5 HELIX 16 16 THR A 311 ARG A 327 1 17 HELIX 17 17 LEU A 328 GLU A 330 5 3 HELIX 18 18 ASP A 332 ASP A 340 1 9 HELIX 19 19 ASP A 340 SER A 348 1 9 HELIX 20 20 THR A 351 ASN A 360 1 10 HELIX 21 21 ASP A 362 GLY A 370 1 9 HELIX 22 22 ILE A 372 LEU A 383 1 12 HELIX 23 23 GLY A 386 ARG A 395 1 10 HELIX 24 24 SER A 398 LYS A 404 1 7 HELIX 25 25 THR B 13 ALA B 22 1 10 HELIX 26 26 VAL B 29 LYS B 48 1 20 HELIX 27 27 ASP B 96 ASP B 110 1 15 HELIX 28 28 ASP B 123 LEU B 134 1 12 HELIX 29 29 LYS B 158 TYR B 176 1 19 HELIX 30 30 ASN B 203 ASP B 217 1 15 HELIX 31 31 PRO B 218 LEU B 222 5 5 HELIX 32 32 THR B 225 GLY B 234 1 10 HELIX 33 33 TRP B 235 GLU B 239 5 5 HELIX 34 34 VAL B 240 ALA B 249 1 10 HELIX 35 35 SER B 286 ARG B 296 1 11 HELIX 36 36 GLU B 297 ALA B 299 5 3 HELIX 37 37 GLY B 300 ILE B 304 5 5 HELIX 38 38 THR B 311 ARG B 327 1 17 HELIX 39 39 GLU B 330 ASP B 340 1 11 HELIX 40 40 ASP B 340 SER B 348 1 9 HELIX 41 41 THR B 351 ASN B 360 1 10 HELIX 42 42 ASP B 362 GLY B 370 1 9 HELIX 43 43 ILE B 372 GLY B 384 1 13 HELIX 44 44 ASN B 387 PHE B 394 1 8 HELIX 45 45 SER B 398 GLN B 403 1 6 SHEET 1 A 9 HIS A 258 PHE A 262 0 SHEET 2 A 9 ILE A 269 LEU A 273 -1 O ILE A 269 N PHE A 262 SHEET 3 A 9 LYS A 3 VAL A 10 -1 N ALA A 9 O MET A 272 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 ASN A 57 1 N VAL A 55 O ALA A 185 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 TRP A 117 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 GLN B 148 N ALA B 71 SHEET 5 B 9 VAL B 51 TYR B 56 1 N TYR B 56 O CYS B 149 SHEET 6 B 9 LYS B 181 THR B 187 1 O ALA B 183 N VAL B 51 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 MET B 272 N ALA B 9 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 FE2 A 501 1555 1555 2.70 LINK ND2 ASN A 57 FE FE2 A 501 1555 1555 2.52 LINK NE2 HIS A 59 FE FE2 A 501 1555 1555 2.04 LINK OE1 GLU A 239 FE FE2 A 501 1555 1555 2.05 LINK NE2 HIS B 12 FE FE2 B 501 1555 1555 2.28 LINK ND2 ASN B 57 FE FE2 B 501 1555 1555 2.09 LINK NE2 HIS B 59 FE FE2 B 501 1555 1555 2.11 LINK OE1 GLU B 239 FE FE2 B 501 1555 1555 2.08 CISPEP 1 HIS A 154 PRO A 155 0 4.66 CISPEP 2 GLY A 189 LEU A 190 0 -4.63 CISPEP 3 HIS B 154 PRO B 155 0 12.11 CISPEP 4 GLY B 189 LEU B 190 0 -8.88 SITE 1 AC1 4 HIS A 12 ASN A 57 HIS A 59 GLU A 239 SITE 1 AC2 11 GLU A 377 ASN A 387 TYR A 391 TYR A 412 SITE 2 AC2 11 THR B 13 PRO B 14 HIS B 59 HIS B 124 SITE 3 AC2 11 HIS B 192 MET B 266 THR B 267 SITE 1 AC3 4 HIS B 12 ASN B 57 HIS B 59 GLU B 239 CRYST1 58.350 64.020 118.483 90.00 97.14 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 0.017138 0.000000 0.002148 0.00000 SCALE2 0.000000 0.015620 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008506 0.00000