HEADER OXIDOREDUCTASE 03-JAN-12 3VCA TITLE QUATERNARY AMMONIUM OXIDATIVE DEMETHYLATION: X-RAY CRYSTALLOGRAPHIC, TITLE 2 RESONANCE RAMAN AND UV-VISIBLE SPECTROSCOPIC ANALYSIS OF A RIESKE- TITLE 3 TYPE DEMETHYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RING-HYDROXYLATING DIOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SINORHIZOBIUM MELILOTI; SOURCE 3 ORGANISM_COMMON: ENSIFER MELILOTI; SOURCE 4 ORGANISM_TAXID: 266834; SOURCE 5 STRAIN: 1021; SOURCE 6 GENE: NP_435646, RA0400, SMA0751; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PASK-IBA5+ KEYWDS RIESKE-TYPE, MONONUCLEAR NON-HEME IRON, N-DEMETHYLASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.D.DAUGHTRY,Y.XIAO,D.STONER-MA,E.CHO,A.M.ORVILLE,P.LIU,K.N.ALLEN REVDAT 3 30-OCT-24 3VCA 1 REMARK LINK REVDAT 2 22-FEB-12 3VCA 1 JRNL REVDAT 1 08-FEB-12 3VCA 0 JRNL AUTH K.D.DAUGHTRY,Y.XIAO,D.STONER-MA,E.CHO,A.M.ORVILLE,P.LIU, JRNL AUTH 2 K.N.ALLEN JRNL TITL QUATERNARY AMMONIUM OXIDATIVE DEMETHYLATION: X-RAY JRNL TITL 2 CRYSTALLOGRAPHIC, RESONANCE RAMAN, AND UV-VISIBLE JRNL TITL 3 SPECTROSCOPIC ANALYSIS OF A RIESKE-TYPE DEMETHYLASE. JRNL REF J.AM.CHEM.SOC. V. 134 2823 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 22224443 JRNL DOI 10.1021/JA2111898 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.2_432) 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 65657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 6532 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 28.1949 - 3.4244 1.00 6549 739 0.1670 0.1641 REMARK 3 2 3.4244 - 2.7188 0.99 6176 683 0.1715 0.1859 REMARK 3 3 2.7188 - 2.3753 0.97 6020 669 0.1830 0.2018 REMARK 3 4 2.3753 - 2.1582 0.97 5968 694 0.1695 0.1978 REMARK 3 5 2.1582 - 2.0036 0.98 5980 678 0.1701 0.1901 REMARK 3 6 2.0036 - 1.8855 0.96 5846 614 0.1731 0.2030 REMARK 3 7 1.8855 - 1.7911 0.94 5724 615 0.1805 0.2138 REMARK 3 8 1.7911 - 1.7131 0.94 5619 691 0.1814 0.2182 REMARK 3 9 1.7131 - 1.6472 0.93 5581 655 0.1875 0.2238 REMARK 3 10 1.6472 - 1.5903 0.92 5662 494 0.1964 0.2451 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 36.35 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37900 REMARK 3 B22 (A**2) : 0.37900 REMARK 3 B33 (A**2) : -0.75800 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 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 : 0.006 3296 REMARK 3 ANGLE : 1.180 4496 REMARK 3 CHIRALITY : 0.075 487 REMARK 3 PLANARITY : 0.005 582 REMARK 3 DIHEDRAL : 13.630 1203 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 3VCA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069864. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-08; 05-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS REMARK 200 BEAMLINE : X12C; X12C REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0; 1.738 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL-CUT CRYSTAL; REMARK 200 SI(111) CHANNEL-CUT CRYSTAL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; ADSC QUANTUM REMARK 200 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68467 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 28.191 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 16.30 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 40.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES BUFFER, 10 % PEG 3350, 10 REMARK 280 % GLYCEROL, 25 MM HEXAMINE COBALT, PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 89.66250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 89.66250 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 89.66250 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 89.66250 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 89.66250 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 89.66250 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -129.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 48.83350 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 84.58210 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -48.83350 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 84.58210 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 951 LIES ON A SPECIAL POSITION. 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 THR A 2 REMARK 465 ALA A 3 REMARK 465 ASN A 4 REMARK 465 PRO A 5 REMARK 465 GLN A 226 REMARK 465 ALA A 227 REMARK 465 ASP A 228 REMARK 465 GLY A 229 REMARK 465 ARG A 407 REMARK 465 GLN A 408 REMARK 465 VAL A 409 REMARK 465 ALA A 410 REMARK 465 ALA A 411 REMARK 465 GLU A 412 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 VAL A 225 CG1 CG2 REMARK 470 PRO A 406 CG 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 NH2 ARG A 214 O HOH A 839 1.57 REMARK 500 O HOH A 1160 O HOH A 1177 2.00 REMARK 500 O HOH A 957 O HOH A 966 2.07 REMARK 500 O HOH A 1062 O HOH A 1169 2.10 REMARK 500 O HOH A 714 O HOH A 1054 2.12 REMARK 500 O HOH A 1043 O HOH A 1159 2.13 REMARK 500 NE ARG A 260 O HOH A 1149 2.15 REMARK 500 O HOH A 923 O HOH A 969 2.19 REMARK 500 O HOH A 967 O HOH A 1180 2.19 REMARK 500 NH2 ARG A 260 O HOH A 1149 2.19 REMARK 500 O HOH A 832 O HOH A 967 2.19 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 ILE A 39 -70.12 -115.19 REMARK 500 ALA A 47 -74.40 -106.77 REMARK 500 HIS A 88 -84.17 -80.08 REMARK 500 VAL A 222 -73.35 -77.40 REMARK 500 ALA A 249 -30.96 -142.81 REMARK 500 GLU A 268 103.36 -19.76 REMARK 500 LYS A 269 -9.86 73.24 REMARK 500 VAL A 342 -60.15 -122.53 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 FES A 501 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 86 SG REMARK 620 2 FES A 501 S1 108.8 REMARK 620 3 FES A 501 S2 112.0 105.7 REMARK 620 4 CYS A 106 SG 107.6 108.5 114.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 501 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 88 ND1 REMARK 620 2 FES A 501 S1 111.7 REMARK 620 3 FES A 501 S2 114.0 105.9 REMARK 620 4 HIS A 109 ND1 89.5 112.4 122.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 204 NE2 REMARK 620 2 HIS A 209 NE2 96.0 REMARK 620 3 ASP A 360 OD1 103.1 90.4 REMARK 620 4 HOH A 887 O 96.0 165.4 94.9 REMARK 620 5 HOH A 953 O 90.3 103.0 160.0 68.6 REMARK 620 6 HOH A 960 O 143.8 89.7 112.7 75.8 53.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PRO A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VCP RELATED DB: PDB DBREF 3VCA A 1 412 UNP Q92ZP9 Q92ZP9_RHIME 1 412 SEQRES 1 A 412 MET THR ALA ASN PRO THR SER ILE HIS GLN ARG LEU ASP SEQRES 2 A 412 ARG ARG LEU SER GLY PHE SER LEU GLU GLN PRO PHE TYR SEQRES 3 A 412 THR SER PRO GLU VAL TYR ALA LEU ASP LEU GLN HIS ILE SEQRES 4 A 412 PHE TYR LYS GLN TRP LEU TYR ALA VAL PRO VAL CYS GLN SEQRES 5 A 412 LEU ALA LYS ALA GLY SER TYR THR THR LEU ARG VAL GLY SEQRES 6 A 412 ALA TYR GLU VAL VAL ILE VAL ARG SER ARG ASP GLY GLU SEQRES 7 A 412 VAL ARG ALA PHE HIS ASN SER CYS ARG HIS ARG GLY SER SEQRES 8 A 412 LEU ILE CYS LYS ALA ARG GLN GLY GLN VAL ALA LYS LEU SEQRES 9 A 412 VAL CYS PRO TYR HIS GLN TRP THR TYR GLU LEU ASP GLY SEQRES 10 A 412 LYS LEU ILE TRP ALA ASN ASP MET GLY PRO ASP PHE ASP SEQRES 11 A 412 ALA SER LYS TYR GLY LEU LYS PRO VAL ASN LEU ARG ASN SEQRES 12 A 412 LEU ASP GLY LEU ILE TYR ILE CYS LEU SER ASP THR PRO SEQRES 13 A 412 PRO ASP PHE GLN THR PHE ALA GLN LEU ALA ARG PRO TYR SEQRES 14 A 412 LEU GLU VAL HIS ASP LEU LYS ASP ALA LYS VAL ALA PHE SEQRES 15 A 412 THR SER THR ILE ILE GLU LYS GLY ASN TRP LYS LEU VAL SEQRES 16 A 412 TRP GLU ASN ASN ARG GLU CYS TYR HIS CYS SER SER ASN SEQRES 17 A 412 HIS PRO ALA LEU CYS ARG SER PHE PRO LEU ASP PRO GLU SEQRES 18 A 412 VAL ALA GLY VAL GLN ALA ASP GLY GLY VAL SER LYS LYS SEQRES 19 A 412 LEU GLN ALA HIS PHE ASP ARG CYS GLU ALA ALA GLY THR SEQRES 20 A 412 PRO ALA GLN PHE VAL LEU ALA GLY ASP GLY GLN TYR ARG SEQRES 21 A 412 LEU ALA ARG MET PRO LEU GLN GLU LYS ALA LEU SER TYR SEQRES 22 A 412 THR MET ASP GLY LYS ALA ALA VAL SER ARG HIS LEU GLY SEQRES 23 A 412 ARG VAL ALA PRO PRO ASP ALA GLY THR LEU LEU MET PHE SEQRES 24 A 412 HIS TYR PRO SER THR TRP ASN HIS PHE LEU PRO ASP HIS SEQRES 25 A 412 SER LEU THR PHE ARG VAL MET PRO ILE SER PRO THR GLU SEQRES 26 A 412 THR GLU VAL THR THR THR TRP LEU VAL HIS LYS ASP ALA SEQRES 27 A 412 VAL GLU GLY VAL ASP TYR ASP LEU LYS ARG LEU THR GLU SEQRES 28 A 412 VAL TRP ILE ALA THR ASN ASP GLU ASP ARG GLU ILE VAL SEQRES 29 A 412 GLU THR ASN GLN GLN GLY ILE LEU SER PRO ALA TYR VAL SEQRES 30 A 412 PRO GLY PRO TYR SER PRO GLY GLN GLU SER GLY VAL MET SEQRES 31 A 412 GLN PHE VAL ASP TRP TYR ALA ALA SER LEU GLU ARG ALA SEQRES 32 A 412 LEU ALA PRO ARG GLN VAL ALA ALA GLU HET FES A 501 4 HET FE A 502 1 HET GOL A 503 6 HET PRO A 504 8 HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETNAM FE FE (III) ION HETNAM GOL GLYCEROL HETNAM PRO PROLINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FES FE2 S2 FORMUL 3 FE FE 3+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 PRO C5 H9 N O2 FORMUL 6 HOH *610(H2 O) HELIX 1 1 SER A 7 ARG A 15 1 9 HELIX 2 2 GLU A 22 SER A 28 1 7 HELIX 3 3 SER A 28 ILE A 39 1 12 HELIX 4 4 CYS A 51 ALA A 54 5 4 HELIX 5 5 ASP A 130 TYR A 134 5 5 HELIX 6 6 PHE A 159 VAL A 172 1 14 HELIX 7 7 HIS A 173 LYS A 176 5 4 HELIX 8 8 ASN A 191 ARG A 200 1 10 HELIX 9 9 HIS A 204 HIS A 209 1 6 HELIX 10 10 HIS A 209 ARG A 214 1 6 HELIX 11 11 ASP A 219 GLY A 224 1 6 HELIX 12 12 SER A 232 ALA A 245 1 14 HELIX 13 13 ASP A 345 LEU A 372 1 28 HELIX 14 14 GLU A 386 ALA A 405 1 20 SHEET 1 A 7 LEU A 45 PRO A 49 0 SHEET 2 A 7 LEU A 147 CYS A 151 -1 O ILE A 148 N ALA A 47 SHEET 3 A 7 PRO A 138 LEU A 144 -1 N LEU A 144 O LEU A 147 SHEET 4 A 7 VAL A 79 HIS A 83 -1 N ALA A 81 O VAL A 139 SHEET 5 A 7 TYR A 67 ARG A 73 -1 N VAL A 72 O ARG A 80 SHEET 6 A 7 SER A 58 VAL A 64 -1 N LEU A 62 O VAL A 69 SHEET 7 A 7 GLN A 98 GLN A 100 -1 O GLY A 99 N TYR A 59 SHEET 1 B 3 LEU A 104 VAL A 105 0 SHEET 2 B 3 THR A 112 TYR A 113 -1 O TYR A 113 N LEU A 104 SHEET 3 B 3 LEU A 119 TRP A 121 -1 O TRP A 121 N THR A 112 SHEET 1 C 7 ALA A 178 GLU A 188 0 SHEET 2 C 7 GLU A 325 HIS A 335 -1 O THR A 326 N GLU A 188 SHEET 3 C 7 SER A 313 SER A 322 -1 N MET A 319 O GLU A 327 SHEET 4 C 7 THR A 304 PHE A 308 -1 N HIS A 307 O LEU A 314 SHEET 5 C 7 THR A 295 HIS A 300 -1 N LEU A 296 O PHE A 308 SHEET 6 C 7 TYR A 259 MET A 264 -1 N ALA A 262 O LEU A 297 SHEET 7 C 7 VAL A 252 LEU A 253 -1 N VAL A 252 O LEU A 261 SSBOND 1 CYS A 202 CYS A 205 1555 1555 2.04 LINK SG CYS A 86 FE2 FES A 501 1555 1555 2.36 LINK ND1 HIS A 88 FE1 FES A 501 1555 1555 2.17 LINK SG CYS A 106 FE2 FES A 501 1555 1555 2.33 LINK ND1 HIS A 109 FE1 FES A 501 1555 1555 2.16 LINK NE2 HIS A 204 FE FE A 502 1555 1555 2.15 LINK NE2 HIS A 209 FE FE A 502 1555 1555 2.09 LINK OD1 ASP A 360 FE FE A 502 1555 1555 1.99 LINK FE FE A 502 O HOH A 887 1555 1555 2.13 LINK FE FE A 502 O HOH A 953 1555 1555 2.56 LINK FE FE A 502 O HOH A 960 1555 1555 2.41 CISPEP 1 ALA A 289 PRO A 290 0 -0.97 CISPEP 2 TYR A 301 PRO A 302 0 7.54 SITE 1 AC1 7 CYS A 86 HIS A 88 ARG A 89 SER A 91 SITE 2 AC1 7 CYS A 106 HIS A 109 TRP A 111 SITE 1 AC2 6 HIS A 204 HIS A 209 ASP A 360 HOH A 887 SITE 2 AC2 6 HOH A 953 HOH A 960 SITE 1 AC3 6 ARG A 14 ARG A 15 LEU A 16 GLU A 22 SITE 2 AC3 6 HOH A 620 HOH A1039 SITE 1 AC4 5 THR A 61 GLU A 68 LEU A 92 LYS A 95 SITE 2 AC4 5 ARG A 97 CRYST1 97.667 97.667 179.325 90.00 90.00 120.00 P 63 2 2 12 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 0.010239 0.005911 0.000000 0.00000 SCALE2 0.000000 0.011823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005576 0.00000