HEADER OXIDOREDUCTASE 13-FEB-14 3WR4 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 3WR4 1 REMARK LINK REVDAT 2 14-FEB-18 3WR4 1 REMARK REVDAT 1 30-APR-14 3WR4 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 : 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.1 REMARK 3 NUMBER OF REFLECTIONS : 31674 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1583 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 19.9911 - 6.4448 0.98 3077 169 0.1559 0.2275 REMARK 3 2 6.4448 - 5.1441 0.99 3111 165 0.1861 0.2475 REMARK 3 3 5.1441 - 4.5023 0.97 3050 164 0.1779 0.2556 REMARK 3 4 4.5023 - 4.0945 0.96 2986 164 0.1743 0.2438 REMARK 3 5 4.0945 - 3.8032 0.96 2996 156 0.2075 0.2307 REMARK 3 6 3.8032 - 3.5803 0.95 3008 158 0.2136 0.2968 REMARK 3 7 3.5803 - 3.4019 0.94 2989 159 0.2239 0.2968 REMARK 3 8 3.4019 - 3.2545 0.94 2944 155 0.2409 0.3033 REMARK 3 9 3.2545 - 3.1297 0.92 2895 149 0.2537 0.3783 REMARK 3 10 3.1297 - 3.0221 0.91 2873 146 0.2770 0.3992 REMARK 3 11 3.0221 - 2.9279 0.89 2772 150 0.2824 0.3065 REMARK 3 12 2.9279 - 2.8444 0.86 2731 149 0.2722 0.4095 REMARK 3 13 2.8444 - 2.7698 0.85 2651 134 0.2775 0.3925 REMARK 3 14 2.7698 - 2.7023 0.81 2557 131 0.2933 0.3997 REMARK 3 15 2.7023 - 2.6410 0.79 2468 129 0.3109 0.3908 REMARK 3 16 2.6410 - 2.5850 0.74 2336 129 0.3191 0.4182 REMARK 3 17 2.5850 - 2.5334 0.75 2341 125 0.3137 0.3761 REMARK 3 18 2.5334 - 2.4856 0.70 2195 109 0.3068 0.3939 REMARK 3 19 2.4856 - 2.4413 0.67 2114 109 0.3357 0.4474 REMARK 3 20 2.4413 - 2.4000 0.64 1984 114 0.3591 0.4289 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) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.90 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 6650 REMARK 3 ANGLE : 1.314 9020 REMARK 3 CHIRALITY : 0.051 932 REMARK 3 PLANARITY : 0.006 1188 REMARK 3 DIHEDRAL : 15.581 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 3WR4 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_1000096687. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-APR-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) : 1.73912 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 : 56954 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 85.9 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) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.4 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 (%): 47.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 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 31.95250 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: 9750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 O ARG A 160 ND2 ASN A 164 2.15 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 GLU A 38 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 LEU A 263 CA - CB - CG ANGL. DEV. = 14.6 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 THR A 13 133.75 -38.11 REMARK 500 PRO A 39 5.02 -53.97 REMARK 500 LYS A 48 75.23 44.56 REMARK 500 TYR A 56 -159.17 -127.85 REMARK 500 HIS A 59 62.41 -105.58 REMARK 500 THR A 61 -68.96 -93.61 REMARK 500 PHE A 64 -80.12 -147.51 REMARK 500 GLN A 87 92.65 -64.59 REMARK 500 ASP A 89 94.60 -69.49 REMARK 500 GLU A 111 40.76 72.09 REMARK 500 SER A 131 39.07 -75.92 REMARK 500 VAL A 132 -26.88 -160.28 REMARK 500 PRO A 135 108.18 -52.55 REMARK 500 ASP A 179 75.56 -68.09 REMARK 500 LEU A 190 -133.34 -101.62 REMARK 500 GLN A 193 114.95 -163.73 REMARK 500 ALA A 199 86.74 -49.04 REMARK 500 ASN A 203 118.18 -168.35 REMARK 500 VAL A 240 0.77 -60.56 REMARK 500 THR A 256 67.80 -52.77 REMARK 500 GLN A 259 99.94 -173.29 REMARK 500 TYR A 261 153.80 172.93 REMARK 500 PHE A 262 125.94 161.14 REMARK 500 PRO A 264 -102.21 -71.02 REMARK 500 SER A 265 -105.76 -72.72 REMARK 500 ALA A 268 93.95 -61.77 REMARK 500 GLN A 277 -142.81 -85.19 REMARK 500 ALA A 280 -80.58 -45.69 REMARK 500 PRO A 282 124.96 -35.07 REMARK 500 ASP A 340 77.01 -117.78 REMARK 500 SER A 348 -177.72 -58.76 REMARK 500 HIS B 59 68.99 -112.31 REMARK 500 THR B 61 -76.94 -106.87 REMARK 500 PHE B 64 -78.77 -141.05 REMARK 500 ASP B 96 82.21 -150.74 REMARK 500 HIS B 136 20.92 -148.25 REMARK 500 GLU B 137 0.77 -62.65 REMARK 500 HIS B 138 -34.74 -166.38 REMARK 500 LEU B 190 -123.90 -84.75 REMARK 500 HIS B 192 151.84 163.67 REMARK 500 ASN B 203 88.81 -162.35 REMARK 500 ASP B 217 52.89 -164.56 REMARK 500 VAL B 240 1.35 -60.78 REMARK 500 SER B 265 -118.48 -127.65 REMARK 500 ALA B 268 93.68 -54.98 REMARK 500 ALA B 280 -83.70 -64.67 REMARK 500 GLU B 303 47.04 -94.75 REMARK 500 ASP B 340 64.59 -151.10 REMARK 500 LEU B 397 170.29 -54.97 REMARK 500 THR B 405 -47.11 -155.89 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 138 148.50 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 ASN A 57 ND2 73.8 REMARK 620 3 HIS A 59 NE2 80.1 104.2 REMARK 620 4 GLU A 239 OE1 106.7 68.1 166.9 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 ND2 89.4 REMARK 620 3 HIS B 59 NE2 106.2 110.1 REMARK 620 4 GLU B 239 OE1 88.9 67.2 164.8 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 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: 3WR3 RELATED DB: PDB DBREF 3WR4 A 1 418 UNP G2IKE5 G2IKE5_9SPHN 1 418 DBREF 3WR4 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 1 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 HELIX 1 1 THR A 13 ALA A 17 5 5 HELIX 2 2 TRP A 30 GLN A 35 1 6 HELIX 3 3 PHE A 37 GLN A 47 1 11 HELIX 4 4 ASP A 96 ASP A 110 1 15 HELIX 5 5 ASP A 123 SER A 131 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 ALA A 249 1 10 HELIX 12 12 SER A 286 ARG A 296 1 11 HELIX 13 13 GLU A 297 ALA A 299 5 3 HELIX 14 14 GLY A 300 ILE A 304 5 5 HELIX 15 15 THR A 311 ARG A 327 1 17 HELIX 16 16 LEU A 328 GLU A 330 5 3 HELIX 17 17 ASP A 332 ASP A 340 1 9 HELIX 18 18 ASP A 340 SER A 348 1 9 HELIX 19 19 THR A 351 ASN A 360 1 10 HELIX 20 20 ASP A 362 GLY A 370 1 9 HELIX 21 21 ILE A 372 LEU A 383 1 12 HELIX 22 22 GLY A 386 GLY A 396 1 11 HELIX 23 23 SER A 398 LYS A 404 1 7 HELIX 24 24 THR B 13 ALA B 22 1 10 HELIX 25 25 TRP B 30 LYS B 48 1 19 HELIX 26 26 ASP B 96 ASP B 110 1 15 HELIX 27 27 ASP B 123 LEU B 134 1 12 HELIX 28 28 LYS B 158 TYR B 176 1 19 HELIX 29 29 ASN B 203 ASP B 217 1 15 HELIX 30 30 PRO B 218 LEU B 222 5 5 HELIX 31 31 THR B 225 GLY B 234 1 10 HELIX 32 32 TRP B 235 GLU B 239 5 5 HELIX 33 33 VAL B 240 ALA B 249 1 10 HELIX 34 34 SER B 286 ARG B 296 1 11 HELIX 35 35 GLU B 297 ALA B 299 5 3 HELIX 36 36 GLY B 300 ILE B 304 5 5 HELIX 37 37 THR B 311 GLY B 318 1 8 HELIX 38 38 GLY B 318 ARG B 327 1 10 HELIX 39 39 GLU B 330 LYS B 335 1 6 HELIX 40 40 LYS B 335 ASP B 340 1 6 HELIX 41 41 ASP B 340 PHE B 345 1 6 HELIX 42 42 THR B 351 ASN B 360 1 10 HELIX 43 43 ASP B 362 GLY B 370 1 9 HELIX 44 44 ILE B 372 LEU B 383 1 12 HELIX 45 45 GLY B 386 GLY B 396 1 11 HELIX 46 46 SER B 398 LYS B 404 1 7 SHEET 1 A 8 THR A 271 LEU A 273 0 SHEET 2 A 8 LYS A 3 VAL A 10 -1 N ALA A 9 O MET A 272 SHEET 3 A 8 LYS A 181 THR A 187 1 O GLY A 186 N PHE A 8 SHEET 4 A 8 VAL A 51 ASN A 57 1 N VAL A 51 O ALA A 183 SHEET 5 A 8 ARG A 143 CYS A 149 1 O ARG A 143 N THR A 52 SHEET 6 A 8 PHE A 70 GLY A 73 -1 N ALA A 71 O GLN A 148 SHEET 7 A 8 ALA A 115 TRP A 117 1 O ALA A 115 N LEU A 72 SHEET 8 A 8 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 THR B 52 O ARG B 143 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 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 FE A 501 1555 1555 2.79 LINK ND2 ASN A 57 FE FE A 501 1555 1555 2.56 LINK NE2 HIS A 59 FE FE A 501 1555 1555 2.35 LINK OE1 GLU A 239 FE FE A 501 1555 1555 2.05 LINK NE2 HIS B 12 FE FE B 501 1555 1555 2.38 LINK ND2 ASN B 57 FE FE B 501 1555 1555 2.36 LINK NE2 HIS B 59 FE FE B 501 1555 1555 2.08 LINK OE1 GLU B 239 FE FE B 501 1555 1555 2.10 CISPEP 1 HIS A 154 PRO A 155 0 1.46 CISPEP 2 GLY A 189 LEU A 190 0 -4.84 CISPEP 3 HIS B 154 PRO B 155 0 8.86 CISPEP 4 GLY B 189 LEU B 190 0 -10.41 SITE 1 AC1 4 HIS A 12 ASN A 57 HIS A 59 GLU A 239 SITE 1 AC2 4 HIS B 12 ASN B 57 HIS B 59 GLU B 239 SITE 1 AC3 10 GLU A 377 TYR A 391 TYR A 412 THR B 13 SITE 2 AC3 10 PRO B 14 HIS B 59 HIS B 124 HIS B 192 SITE 3 AC3 10 MET B 266 THR B 267 CRYST1 58.303 63.905 118.295 90.00 96.98 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 0.017152 0.000000 0.002100 0.00000 SCALE2 0.000000 0.015648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008517 0.00000