HEADER OXIDOREDUCTASE 08-OCT-01 1GNT TITLE HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS. X-RAY STRUCTURE AT TITLE 2 1.25A RESOLUTION USING SYNCHROTRON RADIATION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYBRID CLUSTER PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HCP; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CUBANE CLUSTER [4FE-4S] HYBRID CLUSTER [4FE-3S-3O] COMPND 7 PERSULPHIDE BOND BETWEEN S7 (HYBRID CLUSTER) AND S OF CYS406 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 3 ORGANISM_TAXID: 881; SOURCE 4 STRAIN: HILDENBOROUGH NCIMB8303; SOURCE 5 EXPRESSION_SYSTEM: DESULFOVIBRIO VULGARIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 881; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HILDENBOROUGH NCIMB8303; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PJSP104 KEYWDS OXIDOREDUCTASE, HYBRID CLUSTER PROTEIN, AEROBIC DESULFOVIBRIO KEYWDS 2 VULGARIS EXPDTA X-RAY DIFFRACTION AUTHOR S.MACEDO,E.P.MITCHELL,C.V.ROMAO,S.J.COOPER,R.COELHO,M.Y.LIU, AUTHOR 2 A.V.XAVIER,J.LEGALL,S.BAILEY,D.C.GARNER,W.R.HAGEN,M.TEIXEIRA, AUTHOR 3 M.A.CARRONDO,P.LINDLEY REVDAT 5 13-DEC-23 1GNT 1 REMARK REVDAT 4 23-DEC-20 1GNT 1 LINK REVDAT 3 06-FEB-19 1GNT 1 JRNL REMARK REVDAT 2 24-FEB-09 1GNT 1 VERSN REVDAT 1 11-APR-02 1GNT 0 JRNL AUTH S.MACEDO,E.P.MITCHELL,C.V.ROMAO,S.J.COOPER,R.COELHO,M.Y.LIU, JRNL AUTH 2 A.V.XAVIER,J.LEGALL,S.BAILEY,D.C.GARNER,W.R.HAGEN, JRNL AUTH 3 M.TEIXEIRA,M.A.CARRONDO,P.LINDLEY JRNL TITL HYBRID CLUSTER PROTEINS (HCPS) FROM DESULFOVIBRIO JRNL TITL 2 DESULFURICANS ATCC 27774 AND DESULFOVIBRIO VULGARIS JRNL TITL 3 (HILDENBOROUGH): X-RAY STRUCTURES AT 1.25 A RESOLUTION USING JRNL TITL 4 SYNCHROTRON RADIATION. JRNL REF J. BIOL. INORG. CHEM. V. 7 514 2002 JRNL REFN ISSN 0949-8257 JRNL PMID 11941509 JRNL DOI 10.1007/S00775-001-0326-Y REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0.36 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 155271 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 8216 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10111 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2840 REMARK 3 BIN FREE R VALUE SET COUNT : 548 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4217 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 1015 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.041 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.042 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.978 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4346 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4013 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): 5891 ; 1.467 ; 1.969 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 9372 ; 1.168 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 678 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4826 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 822 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 942 ; 0.231 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3704 ; 0.180 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 3 ; 0.339 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 687 ; 0.197 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 11 ; 0.277 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 36 ; 0.217 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 67 ; 0.366 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2748 ; 0.693 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4421 ; 1.217 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1598 ; 1.895 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1470 ; 3.064 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1GNT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1290008674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1999 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : SI(111) BENT TRIANGULAR REMARK 200 OPTICS : PLATINUM COATED FUSED QUARTZ REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 163543 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 19.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33100 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB FROM ENTRY 1E2U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25-30% PEG 8000 0.1M MES PH 5.9, 0.2M REMARK 280 MAGNESIUM ACETATE, T=277K, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 31.90500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.93500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.26500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.93500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.90500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.26500 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 HOH A 2979 O HOH A 2982 1.78 REMARK 500 O HOH A 2027 O HOH A 2867 1.87 REMARK 500 O HOH A 2991 O HOH A 2993 1.95 REMARK 500 OE2 GLU A 300 OG1 THR A 321 1.97 REMARK 500 NZ LYS A 105 O HOH A 2347 1.99 REMARK 500 O HOH A 2714 O HOH A 2717 2.06 REMARK 500 OE1 GLU A 26 O HOH A 2075 2.06 REMARK 500 NZ LYS A 318 O HOH A 2742 2.08 REMARK 500 O HOH A 2198 O HOH A 2249 2.10 REMARK 500 O HOH A 2521 O HOH A 2935 2.11 REMARK 500 OD1 ASP A 60 O HOH A 2201 2.11 REMARK 500 O HOH A 2427 O HOH A 2821 2.13 REMARK 500 O HOH A 2521 O HOH A 2932 2.13 REMARK 500 OE2 GLU A 142 O HOH A 2471 2.14 REMARK 500 O HOH A 2091 O HOH A 2092 2.14 REMARK 500 O HOH A 2379 O HOH A 2384 2.15 REMARK 500 O HOH A 2480 O HOH A 2481 2.16 REMARK 500 O HOH A 2666 O HOH A 2698 2.16 REMARK 500 OE2 GLU A 257 O HOH A 2686 2.17 REMARK 500 O HOH A 2489 O HOH A 2907 2.17 REMARK 500 OE2 GLU A 25 O HOH A 2072 2.18 REMARK 500 O HOH A 2013 O HOH A 2027 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2409 O HOH A 2522 1545 1.78 REMARK 500 O HOH A 2206 O HOH A 2358 3655 1.92 REMARK 500 O HOH A 2346 O HOH A 2930 3645 2.04 REMARK 500 O HOH A 2128 O HOH A 2512 3645 2.05 REMARK 500 O HOH A 2409 O HOH A 2934 1545 2.10 REMARK 500 O HOH A 2597 O HOH A 2669 1455 2.12 REMARK 500 O HOH A 2379 O HOH A 2859 1545 2.16 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 PHE A 4 22.69 -141.76 REMARK 500 LYS A 11 15.16 59.35 REMARK 500 VAL A 17 -55.15 -121.14 REMARK 500 ASN A 303 -28.75 73.41 REMARK 500 PHE A 376 58.55 -91.57 REMARK 500 ALA A 432 145.51 -171.58 REMARK 500 TYR A 439 12.77 -152.26 REMARK 500 TYR A 493 -59.27 -138.59 REMARK 500 GLU A 494 -157.99 -120.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASN A 296 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2005 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A2009 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A2024 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A2029 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A2039 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH A2040 DISTANCE = 7.40 ANGSTROMS REMARK 525 HOH A2044 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A2080 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A2082 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A2097 DISTANCE = 6.69 ANGSTROMS REMARK 525 HOH A2136 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A2198 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A2216 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A2429 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A2455 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH A2459 DISTANCE = 6.24 ANGSTROMS 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 SF4 A1554 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 3 SG REMARK 620 2 SF4 A1554 S2 119.5 REMARK 620 3 SF4 A1554 S3 107.9 102.3 REMARK 620 4 SF4 A1554 S4 113.8 104.5 107.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A1554 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 SF4 A1554 S1 98.9 REMARK 620 3 SF4 A1554 S2 118.4 110.0 REMARK 620 4 SF4 A1554 S4 120.8 104.6 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A1554 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 15 SG REMARK 620 2 SF4 A1554 S1 110.7 REMARK 620 3 SF4 A1554 S3 109.4 105.3 REMARK 620 4 SF4 A1554 S4 118.3 104.8 107.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A1554 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 21 SG REMARK 620 2 SF4 A1554 S1 107.5 REMARK 620 3 SF4 A1554 S2 116.8 108.9 REMARK 620 4 SF4 A1554 S3 116.7 104.5 101.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FSO A1555 FE7 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 244 NE2 REMARK 620 2 FSO A1555 O9 91.1 REMARK 620 3 FSO A1555 O10 109.5 68.2 REMARK 620 4 GLU A 268 OE2 89.6 178.8 112.4 REMARK 620 5 CYS A 459 SG 106.4 86.9 136.2 91.9 REMARK 620 6 FSO A1555 O10 109.5 68.2 0.0 112.4 136.2 REMARK 620 7 FSO A1555 O10 133.6 91.4 32.3 88.8 120.0 32.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FSO A1555 FE6 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 312 SG REMARK 620 2 FSO A1555 S5 132.1 REMARK 620 3 FSO A1555 S6 112.5 107.3 REMARK 620 4 FSO A1555 O8 106.3 95.3 95.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FSO A1555 FE5 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 434 SG REMARK 620 2 FSO A1555 S5 116.8 REMARK 620 3 FSO A1555 S6 103.0 101.6 REMARK 620 4 FSO A1555 O10 135.2 98.7 94.8 REMARK 620 5 FSO A1555 O10 135.2 98.7 94.8 0.0 REMARK 620 6 FSO A1555 O10 101.1 124.3 108.0 34.1 34.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FSO A1555 FE8 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 494 OE2 REMARK 620 2 FSO A1555 S6 114.4 REMARK 620 3 FSO A1555 S7 85.3 91.0 REMARK 620 4 FSO A1555 O8 81.6 87.2 164.6 REMARK 620 5 FSO A1555 O9 92.9 150.7 102.1 86.6 REMARK 620 6 FSO A1555 O10 155.0 83.9 112.5 82.5 66.8 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 SF4 A1554 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FSO A1555 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1E1D RELATED DB: PDB REMARK 900 HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS REMARK 900 RELATED ID: 1E2U RELATED DB: PDB REMARK 900 LOW TEMPERATURE STUCTURE OF HYBRID CLUSTER PROTEIN FROM REMARK 900 DESULFOVIBRIO VULGARIS TO 1.6A REMARK 900 RELATED ID: 1E9V RELATED DB: PDB REMARK 900 XENON BOUND IN HYDROPHOBIC CHANNEL OF HYBRID CLUSTER PROTEIN FROM REMARK 900 DESULFOVIBRIO VULGARIS DBREF 1GNT A 1 553 UNP P31101 HCP_DESVH 1 553 SEQRES 1 A 553 MET PHE CYS PHE GLN CYS GLN GLU THR ALA LYS ASN THR SEQRES 2 A 553 GLY CYS THR VAL LYS GLY MET CYS GLY LYS PRO GLU GLU SEQRES 3 A 553 THR ALA ASN LEU GLN ASP LEU LEU ILE PHE VAL LEU ARG SEQRES 4 A 553 GLY ILE ALA ILE TYR GLY GLU LYS LEU LYS GLU LEU GLY SEQRES 5 A 553 GLN PRO ASP ARG SER ASN ASP ASP PHE VAL LEU GLN GLY SEQRES 6 A 553 LEU PHE ALA THR ILE THR ASN ALA ASN TRP ASP ASP ALA SEQRES 7 A 553 ARG PHE GLU ALA MET ILE SER GLU GLY LEU ALA ARG ARG SEQRES 8 A 553 ASP LYS LEU ARG ASN ALA PHE LEU ALA VAL TYR LYS ALA SEQRES 9 A 553 LYS ASN GLY LYS ASP PHE SER GLU PRO LEU PRO GLU ALA SEQRES 10 A 553 ALA THR TRP THR GLY ASP SER THR ALA PHE ALA GLU LYS SEQRES 11 A 553 ALA LYS SER VAL GLY ILE LEU ALA THR GLU ASN GLU ASP SEQRES 12 A 553 VAL ARG SER LEU ARG GLU LEU LEU ILE ILE GLY LEU LYS SEQRES 13 A 553 GLY VAL ALA ALA TYR ALA GLU HIS ALA ALA VAL LEU GLY SEQRES 14 A 553 PHE ARG LYS THR GLU ILE ASP GLU PHE MET LEU GLU ALA SEQRES 15 A 553 LEU ALA SER THR THR LYS ASP LEU SER VAL ASP GLU MET SEQRES 16 A 553 VAL ALA LEU VAL MET LYS ALA GLY GLY MET ALA VAL THR SEQRES 17 A 553 THR MET ALA LEU LEU ASP GLU ALA ASN THR THR THR TYR SEQRES 18 A 553 GLY ASN PRO GLU ILE THR GLN VAL ASN ILE GLY VAL GLY SEQRES 19 A 553 LYS ASN PRO GLY ILE LEU ILE SER GLY HIS ASP LEU LYS SEQRES 20 A 553 ASP MET ALA GLU LEU LEU LYS GLN THR GLU GLY THR GLY SEQRES 21 A 553 VAL ASP VAL TYR THR HIS GLY GLU MET LEU PRO ALA ASN SEQRES 22 A 553 TYR TYR PRO ALA PHE LYS LYS TYR PRO HIS PHE VAL GLY SEQRES 23 A 553 ASN TYR GLY GLY SER TRP TRP GLN GLN ASN PRO GLU PHE SEQRES 24 A 553 GLU SER PHE ASN GLY PRO ILE LEU LEU THR THR ASN CYS SEQRES 25 A 553 LEU VAL PRO LEU LYS LYS GLU ASN THR TYR LEU ASP ARG SEQRES 26 A 553 LEU TYR THR THR GLY VAL VAL GLY TYR GLU GLY ALA LYS SEQRES 27 A 553 HIS ILE ALA ASP ARG PRO ALA GLY GLY ALA LYS ASP PHE SEQRES 28 A 553 SER ALA LEU ILE ALA GLN ALA LYS LYS CYS PRO PRO PRO SEQRES 29 A 553 VAL GLU ILE GLU THR GLY SER ILE VAL GLY GLY PHE ALA SEQRES 30 A 553 HIS HIS GLN VAL LEU ALA LEU ALA ASP LYS VAL VAL GLU SEQRES 31 A 553 ALA VAL LYS SER GLY ALA ILE LYS ARG PHE VAL VAL MET SEQRES 32 A 553 ALA GLY CYS ASP GLY ARG GLN LYS SER ARG SER TYR TYR SEQRES 33 A 553 THR GLU VAL ALA GLU ASN LEU PRO LYS ASP THR VAL ILE SEQRES 34 A 553 LEU THR ALA GLY CYS ALA LYS TYR ARG TYR ASN LYS LEU SEQRES 35 A 553 ASN LEU GLY ASP ILE GLY GLY ILE PRO ARG VAL LEU ASP SEQRES 36 A 553 ALA GLY GLN CYS ASN ASP SER TYR SER LEU ALA VAL ILE SEQRES 37 A 553 ALA LEU LYS LEU LYS GLU VAL PHE GLY LEU ASP ASP ILE SEQRES 38 A 553 ASN ASP LEU PRO VAL SER TYR ASP ILE ALA TRP TYR GLU SEQRES 39 A 553 GLN LYS ALA VAL ALA VAL LEU LEU ALA LEU LEU PHE LEU SEQRES 40 A 553 GLY VAL LYS GLY ILE ARG LEU GLY PRO THR LEU PRO ALA SEQRES 41 A 553 PHE LEU SER PRO ASN VAL ALA LYS VAL LEU VAL GLU ASN SEQRES 42 A 553 PHE ASN ILE LYS PRO ILE GLY THR VAL GLN ASP ASP ILE SEQRES 43 A 553 ALA ALA MET MET ALA GLY LYS HET SF4 A1554 8 HET FSO A1555 11 HETNAM SF4 IRON/SULFUR CLUSTER HETNAM FSO IRON/SULFUR/OXYGEN HYBRID CLUSTER FORMUL 2 SF4 FE4 S4 FORMUL 3 FSO FE4 O3 S3 FORMUL 4 HOH *1015(H2 O) HELIX 1 1 THR A 9 THR A 13 5 5 HELIX 2 2 PRO A 24 LEU A 51 1 28 HELIX 3 3 ASN A 58 THR A 69 1 12 HELIX 4 4 ASP A 76 GLY A 107 1 32 HELIX 5 5 PRO A 115 THR A 119 5 5 HELIX 6 6 ASP A 123 THR A 125 5 3 HELIX 7 7 ALA A 126 LYS A 132 1 7 HELIX 8 8 GLY A 135 THR A 139 5 5 HELIX 9 9 ASN A 141 LEU A 168 1 28 HELIX 10 10 LYS A 172 THR A 186 1 15 HELIX 11 11 SER A 191 GLY A 222 1 32 HELIX 12 12 ASP A 245 GLU A 257 1 13 HELIX 13 13 GLY A 267 TYR A 274 5 8 HELIX 14 14 TYR A 275 LYS A 280 1 6 HELIX 15 15 SER A 291 TRP A 293 5 3 HELIX 16 16 GLN A 294 ASN A 303 1 10 HELIX 17 17 TYR A 322 ASP A 324 5 3 HELIX 18 18 PHE A 351 LYS A 359 1 9 HELIX 19 19 ALA A 377 LEU A 384 1 8 HELIX 20 20 LEU A 384 SER A 394 1 11 HELIX 21 21 GLN A 410 SER A 412 5 3 HELIX 22 22 ARG A 413 LEU A 423 1 11 HELIX 23 23 GLY A 433 TYR A 439 5 7 HELIX 24 24 GLN A 458 ASN A 460 5 3 HELIX 25 25 ASP A 461 PHE A 476 1 16 HELIX 26 26 ASP A 480 LEU A 484 5 5 HELIX 27 27 GLU A 494 LEU A 507 1 14 HELIX 28 28 SER A 523 ASN A 535 1 13 HELIX 29 29 THR A 541 ALA A 551 1 11 SHEET 1 AA 2 THR A 227 ASN A 230 0 SHEET 2 AA 2 SER A 371 GLY A 374 -1 O ILE A 372 N VAL A 229 SHEET 1 AB 6 PHE A 284 ASN A 287 0 SHEET 2 AB 6 ASP A 262 THR A 265 1 O VAL A 263 N VAL A 285 SHEET 3 AB 6 GLY A 238 SER A 242 1 O ILE A 239 N TYR A 264 SHEET 4 AB 6 ILE A 306 LEU A 308 1 O LEU A 307 N SER A 242 SHEET 5 AB 6 LEU A 326 THR A 329 1 O TYR A 327 N LEU A 308 SHEET 6 AB 6 LYS A 338 ILE A 340 1 O LYS A 338 N THR A 328 SHEET 1 AC 5 VAL A 453 ASP A 455 0 SHEET 2 AC 5 THR A 427 THR A 431 1 O ILE A 429 N LEU A 454 SHEET 3 AC 5 ARG A 399 VAL A 402 1 O ARG A 399 N VAL A 428 SHEET 4 AC 5 VAL A 486 ALA A 491 1 O SER A 487 N VAL A 402 SHEET 5 AC 5 ARG A 513 GLY A 515 1 O ARG A 513 N ILE A 490 SHEET 1 AD 2 ASP A 446 ILE A 447 0 SHEET 2 AD 2 ILE A 450 PRO A 451 -1 O ILE A 450 N ILE A 447 LINK SG CYS A 406 S7 FSO A1555 1555 1555 2.10 LINK SG CYS A 3 FE1 SF4 A1554 1555 1555 2.29 LINK SG CYS A 6 FE3 SF4 A1554 1555 1555 2.27 LINK SG CYS A 15 FE2 SF4 A1554 1555 1555 2.36 LINK SG CYS A 21 FE4 SF4 A1554 1555 1555 2.31 LINK NE2 HIS A 244 FE7 FSO A1555 1555 1555 2.18 LINK OE2 GLU A 268 FE7 FSO A1555 1555 1555 2.16 LINK SG CYS A 312 FE6 FSO A1555 1555 1555 2.31 LINK SG CYS A 434 FE5 FSO A1555 1555 1555 2.32 LINK SG CYS A 459 FE7 FSO A1555 1555 1555 2.45 LINK OE2 GLU A 494 FE8 FSO A1555 1555 1555 2.09 LINK FE7 FSO A1555 O10AFSO A1555 1555 1555 1.86 LINK FE5 FSO A1555 O10AFSO A1555 1555 1555 1.90 LINK FE5 FSO A1555 O10BFSO A1555 1555 1555 1.94 LINK FE7 FSO A1555 O10BFSO A1555 1555 1555 2.10 LINK FE8 FSO A1555 O10AFSO A1555 1555 1555 2.22 CISPEP 1 ASN A 311 CYS A 312 0 3.36 CISPEP 2 GLY A 515 PRO A 516 0 7.42 SITE 1 AC1 11 CYS A 3 PHE A 4 GLN A 5 CYS A 6 SITE 2 AC1 11 THR A 9 CYS A 15 GLY A 19 MET A 20 SITE 3 AC1 11 CYS A 21 LYS A 23 THR A 71 SITE 1 AC2 11 HIS A 244 GLU A 268 ASN A 311 CYS A 312 SITE 2 AC2 11 CYS A 406 CYS A 434 CYS A 459 GLU A 494 SITE 3 AC2 11 LYS A 496 ALA A 497 HOH A2722 CRYST1 63.810 64.530 151.870 90.00 90.00 90.00 P 21 21 21 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 0.015672 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015497 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006585 0.00000