HEADER OXIDOREDUCTASE 27-OCT-00 1E9V TITLE XENON BOUND IN HYDROPHOBIC CHANNEL OF HYBRID CLUSTER PROTEIN FROM TITLE 2 DESULFOVIBRIO VULGARIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROXYLAMINE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HYBRID CLUSTER PROTEIN, PRISMANE PROTEIN, HCP; COMPND 5 EC: 1.7.-.-; COMPND 6 ENGINEERED: YES 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, CUBANE, IRON SULFUR, THIOCYSTEINE, PRISMANE, KEYWDS 2 HYDROPHOBIC CAVITY, S-MERCAPTOCYSTEINE, FUSCOREDOXIN EXPDTA X-RAY DIFFRACTION AUTHOR S.J.COOPER,S.BAILEY,P.J.RIZKALLAH,P.F.LINDLEY REVDAT 5 23-DEC-20 1E9V 1 REMARK LINK ATOM REVDAT 4 27-MAR-13 1E9V 1 SOURCE KEYWDS REMARK SEQADV REVDAT 4 2 1 FORMUL REVDAT 3 26-OCT-11 1E9V 1 COMPND REMARK HETSYN FORMUL REVDAT 3 2 1 VERSN REVDAT 2 24-FEB-09 1E9V 1 VERSN REVDAT 1 25-OCT-01 1E9V 0 JRNL AUTH S.J.COOPER,C.D.GARNER,W.R.HAGEN,P.F.LINDLEY,S.BAILEY JRNL TITL FERRICYANIDE SOAKED HYBRID CLUSTER PROTEIN AT 1.2A AND XENON JRNL TITL 2 MAPPING OF THE HYDROPHOBIC CAVITY AT 1.8A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 56879 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.142 REMARK 3 FREE R VALUE TEST SET COUNT : 2925 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) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : 0.2150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4218 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 748 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): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.024 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 429 ; 0.000 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 582 ; 0.020 ; 0.040 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 369 ; 0.010 ; 0.030 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 14 ; 0.120 ; 0.300 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.270 ; 0.300 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: XE1, XE2, XE7, AND FE, S ATOMS OF FS4 REMARK 3 AND FSO REFINED ANISOTROPICALLY REMARK 4 REMARK 4 1E9V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1290005496. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.90 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX7.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : 70418 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 21.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 5.710 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4368 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.98 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.220 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: CRYSTAL WAS EXPOSED TO XENON AT 15 BAR FOR 30 MINUTES REMARK 200 PRIOR TO FREEZING REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLISED FROM 0.1M MES REMARK 280 PH5.9,60MM MAGNESIUM ACETATE AND 25-30% PEG 8000, PH 5.90 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 31.81000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.12700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.29900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.12700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.81000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.29900 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: PISA 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 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 GLU A 140 CD OE1 OE2 REMARK 480 GLN A 228 CD OE1 NE2 REMARK 480 LYS A 317 CD CE NZ REMARK 480 LYS A 360 CD CE NZ REMARK 480 GLU A 390 CG CD OE1 OE2 REMARK 480 LYS A 411 CG CD CE NZ REMARK 480 ASN A 443 CG OD1 ND2 REMARK 480 GLU A 532 CG CD OE1 OE2 REMARK 480 GLN A 543 CG CD OE1 NE2 REMARK 480 LYS A 553 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 145 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASN A 311 O - C - N ANGL. DEV. = -18.9 DEGREES REMARK 500 CYS A 312 N - CA - CB ANGL. DEV. = 9.5 DEGREES REMARK 500 ASP A 324 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 399 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 409 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 GLY A 515 CA - C - O ANGL. DEV. = -15.5 DEGREES REMARK 500 PRO A 516 CA - N - CD ANGL. DEV. = -9.4 DEGREES REMARK 500 PRO A 516 N - CA - CB ANGL. DEV. = 9.1 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 PHE A 4 25.91 -145.18 REMARK 500 LYS A 11 17.70 57.73 REMARK 500 VAL A 17 -54.10 -120.69 REMARK 500 ASN A 303 -24.09 72.77 REMARK 500 TYR A 439 10.22 -149.72 REMARK 500 ASN A 443 70.48 -115.23 REMARK 500 TYR A 493 -61.25 -138.30 REMARK 500 GLU A 494 -159.37 -112.85 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 ASN A 311 CYS A 312 52.89 REMARK 500 GLY A 515 PRO A 516 48.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN A 311 25.14 REMARK 500 GLY A 515 19.69 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 A2023 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A2053 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A2054 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH A2055 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH A2137 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A2147 DISTANCE = 6.28 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 A 650 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 3 SG REMARK 620 2 SF4 A 650 S2 112.5 REMARK 620 3 SF4 A 650 S3 108.2 108.4 REMARK 620 4 SF4 A 650 S4 119.5 104.5 103.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 650 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 6 SG REMARK 620 2 SF4 A 650 S1 98.7 REMARK 620 3 SF4 A 650 S2 122.1 104.7 REMARK 620 4 SF4 A 650 S4 117.8 109.3 103.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 650 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 15 SG REMARK 620 2 SF4 A 650 S1 111.2 REMARK 620 3 SF4 A 650 S2 117.7 104.7 REMARK 620 4 SF4 A 650 S3 110.8 106.5 105.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 650 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 21 SG REMARK 620 2 SF4 A 650 S1 107.4 REMARK 620 3 SF4 A 650 S3 117.4 106.2 REMARK 620 4 SF4 A 650 S4 114.8 109.1 101.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FSO A 600 FE7 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 244 NE2 REMARK 620 2 FSO A 600 O9 88.7 REMARK 620 3 FSO A 600 O10 154.6 101.5 REMARK 620 4 GLU A 268 OE2 86.9 175.4 83.0 REMARK 620 5 CYS A 459 SG 97.2 86.3 106.5 92.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FSO A 600 FE6 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 312 SG REMARK 620 2 FSO A 600 S5 138.8 REMARK 620 3 FSO A 600 S6 114.5 101.7 REMARK 620 4 FSO A 600 O8 104.8 89.3 96.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FSO A 600 FE8 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CSS A 406 SD REMARK 620 2 FSO A 600 S6 87.2 REMARK 620 3 FSO A 600 O8 165.7 90.1 REMARK 620 4 FSO A 600 O9 106.2 146.6 83.6 REMARK 620 5 GLU A 494 OE2 89.1 126.2 81.2 85.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FSO A 600 FE5 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 434 SG REMARK 620 2 FSO A 600 S5 116.2 REMARK 620 3 FSO A 600 S6 106.6 96.6 REMARK 620 4 FSO A 600 O10 97.8 126.2 112.7 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 FSO A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 650 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 709 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 710 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 711 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XE A 712 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 802 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 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE CYS406 IS MODIFIED TO THIOCYSTEINE DBREF 1E9V A 1 553 UNP P31101 PRIS_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 CSS 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 MODRES 1E9V CSS A 406 CYS S-MERCAPTOCYSTEINE HET CSS A 406 7 HET FSO A 600 9 HET SF4 A 650 8 HET XE A 700 1 HET XE A 701 1 HET XE A 702 1 HET XE A 703 1 HET XE A 704 1 HET XE A 705 1 HET XE A 706 1 HET XE A 707 1 HET XE A 708 1 HET XE A 709 1 HET XE A 710 2 HET XE A 711 1 HET XE A 712 1 HET EDO A 800 4 HET ACY A 801 4 HET GOL A 802 6 HET TRS A 803 8 HETNAM CSS S-MERCAPTOCYSTEINE HETNAM FSO IRON/SULFUR/OXYGEN HYBRID CLUSTER HETNAM SF4 IRON/SULFUR CLUSTER HETNAM XE XENON HETNAM EDO 1,2-ETHANEDIOL HETNAM ACY ACETIC ACID HETNAM GOL GLYCEROL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN TRS TRIS BUFFER FORMUL 1 CSS C3 H7 N O2 S2 FORMUL 2 FSO FE4 O3 S3 FORMUL 3 SF4 FE4 S4 FORMUL 4 XE 13(XE) FORMUL 17 EDO C2 H6 O2 FORMUL 18 ACY C2 H4 O2 FORMUL 19 GOL C3 H8 O3 FORMUL 20 TRS C4 H12 N O3 1+ FORMUL 21 HOH *748(H2 O) HELIX 1 1 ALA A 10 ASN A 12 5 3 HELIX 2 2 GLU A 25 GLU A 50 1 26 HELIX 3 3 ASP A 59 THR A 69 1 11 HELIX 4 4 ASP A 77 ASN A 106 1 30 HELIX 5 5 GLU A 116 ALA A 118 5 3 HELIX 6 6 SER A 124 SER A 133 5 10 HELIX 7 7 ILE A 136 ALA A 138 5 3 HELIX 8 8 GLU A 142 VAL A 167 1 26 HELIX 9 9 THR A 173 THR A 187 1 15 HELIX 10 10 VAL A 192 TYR A 221 1 30 HELIX 11 11 LEU A 246 THR A 256 1 11 HELIX 12 12 GLY A 267 TYR A 274 5 8 HELIX 13 13 PRO A 276 LYS A 279 1 4 HELIX 14 14 TRP A 292 PHE A 302 5 11 HELIX 15 15 LEU A 323 ARG A 325 5 3 HELIX 16 16 SER A 352 LYS A 360 1 9 HELIX 17 17 HIS A 378 SER A 394 1 17 HELIX 18 18 LYS A 411 ASN A 422 5 12 HELIX 19 19 CYS A 434 ARG A 438 5 5 HELIX 20 20 CYS A 459 VAL A 475 5 17 HELIX 21 21 ILE A 481 ASP A 483 5 3 HELIX 22 22 GLN A 495 PHE A 506 1 12 HELIX 23 23 PRO A 524 PHE A 534 1 11 HELIX 24 24 VAL A 542 MET A 550 1 9 SHEET 1 A 2 THR A 227 ASN A 230 0 SHEET 2 A 2 SER A 371 GLY A 374 -1 N GLY A 374 O THR A 227 SHEET 1 B 6 LYS A 338 ILE A 340 0 SHEET 2 B 6 LEU A 326 THR A 329 1 N THR A 328 O LYS A 338 SHEET 3 B 6 ILE A 306 LEU A 308 1 N ILE A 306 O TYR A 327 SHEET 4 B 6 GLY A 238 SER A 242 1 N LEU A 240 O LEU A 307 SHEET 5 B 6 ASP A 262 THR A 265 1 N ASP A 262 O ILE A 239 SHEET 6 B 6 PHE A 284 ASN A 287 1 N VAL A 285 O VAL A 263 SHEET 1 C 4 VAL A 486 TYR A 488 0 SHEET 2 C 4 ARG A 399 VAL A 402 1 N PHE A 400 O SER A 487 SHEET 3 C 4 THR A 427 THR A 431 1 N VAL A 428 O ARG A 399 SHEET 4 C 4 VAL A 453 ASP A 455 1 N LEU A 454 O ILE A 429 SHEET 1 D 2 ASP A 489 ALA A 491 0 SHEET 2 D 2 ARG A 513 GLY A 515 1 N ARG A 513 O ILE A 490 LINK C GLY A 405 N CSS A 406 1555 1555 1.33 LINK C CSS A 406 N ASP A 407 1555 1555 1.32 LINK SG CYS A 3 FE1 SF4 A 650 1555 1555 2.29 LINK SG CYS A 6 FE3 SF4 A 650 1555 1555 2.29 LINK SG CYS A 15 FE4 SF4 A 650 1555 1555 2.33 LINK SG CYS A 21 FE2 SF4 A 650 1555 1555 2.35 LINK NE2 HIS A 244 FE7 FSO A 600 1555 1555 2.21 LINK OE2 GLU A 268 FE7 FSO A 600 1555 1555 2.17 LINK SG CYS A 312 FE6 FSO A 600 1555 1555 2.41 LINK SD CSS A 406 FE8 FSO A 600 1555 1555 2.72 LINK SG CYS A 434 FE5 FSO A 600 1555 1555 2.30 LINK SG CYS A 459 FE7 FSO A 600 1555 1555 2.50 LINK OE2 GLU A 494 FE8 FSO A 600 1555 1555 1.99 SITE 1 AC1 9 HIS A 244 GLU A 268 ASN A 311 CYS A 312 SITE 2 AC1 9 CSS A 406 CYS A 434 CYS A 459 GLU A 494 SITE 3 AC1 9 LYS A 496 SITE 1 AC2 11 CYS A 3 PHE A 4 GLN A 5 CYS A 6 SITE 2 AC2 11 THR A 9 CYS A 15 GLY A 19 MET A 20 SITE 3 AC2 11 CYS A 21 LYS A 23 THR A 71 SITE 1 AC3 2 LEU A 384 VAL A 388 SITE 1 AC4 1 LEU A 501 SITE 1 AC5 1 PHE A 400 SITE 1 AC6 1 LEU A 430 SITE 1 AC7 2 ILE A 490 ALA A 497 SITE 1 AC8 4 ILE A 481 TYR A 488 LEU A 504 VAL A 509 SITE 1 AC9 2 TRP A 492 LEU A 501 SITE 1 BC1 1 SER A 462 SITE 1 BC2 6 ASP A 76 TYR A 334 GLY A 336 ALA A 337 SITE 2 BC2 6 HOH A2163 HOH A2619 SITE 1 BC3 7 THR A 227 ASN A 273 LYS A 279 PHE A 284 SITE 2 BC3 7 HOH A2498 HOH A2503 HOH A2748 SITE 1 BC4 3 GLU A 81 SER A 124 THR A 125 SITE 1 BC5 4 GLU A 181 LYS A 201 HOH A2746 HOH A2747 CRYST1 63.620 64.598 152.254 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 0.015718 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015480 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006568 0.00000