HEADER OXIDOREDUCTASE 29-MAR-13 4JYD TITLE X-RAY SNAPSHOTS OF POSSIBLE INTERMEDIATES IN THE TIME COURSE OF TITLE 2 SYNTHESIS AND DEGRADATION OF PROTEIN-BOUND FE4S4 CLUSTERS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: FEFE-HYDROGENASE MATURASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RADICAL SAM DOMAIN PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 STRAIN: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099; SOURCE 5 GENE: TM_1269, THEMADRAFT_0043; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RADICAL SAM PROTEIN, FEFE-HYDROGENASE ACTIVE SITE ASSEMBLY, FE4S4 KEYWDS 2 CLUSTER, S-ADENOSYL-L-METHIONINE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.NICOLET,R.ROHAC,L.MARTIN,J.C.FONTECILLA-CAMPS REVDAT 2 15-MAY-13 4JYD 1 JRNL REVDAT 1 01-MAY-13 4JYD 0 JRNL AUTH Y.NICOLET,R.ROHAC,L.MARTIN,J.C.FONTECILLA-CAMPS JRNL TITL X-RAY SNAPSHOTS OF POSSIBLE INTERMEDIATES IN THE TIME COURSE JRNL TITL 2 OF SYNTHESIS AND DEGRADATION OF PROTEIN-BOUND FE4S4 JRNL TITL 3 CLUSTERS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 7188 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23596207 JRNL DOI 10.1073/PNAS.1302388110 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 35223 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1879 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) : 1.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2162 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2730 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 195 REMARK 3 SOLVENT ATOMS : 368 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : -0.86000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.272 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.136 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.833 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3072 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2183 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4226 ; 1.843 ; 2.071 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5351 ; 0.988 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 368 ; 6.125 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;33.628 ;23.226 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 523 ;13.324 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;19.086 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 502 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3196 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 580 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 752 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2691 ; 0.213 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1557 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1589 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 269 ; 0.222 ; 0.200 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): 23 ; 0.207 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 93 ; 0.257 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 34 ; 0.218 ; 0.200 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): 1825 ; 1.252 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 711 ; 0.473 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2883 ; 1.734 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1401 ; 2.556 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1320 ; 3.416 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5763 ; 1.791 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 376 ; 6.360 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5166 ; 2.479 ; 3.000 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 : 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 4JYD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-13. REMARK 100 THE RCSB ID CODE IS RCSB078659. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68817 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 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) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.1 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS; 200 MM LI2SO4; 30% REMARK 280 PEG4000, PH 8, VAPOR DIFFUSION, HANGING DROP, 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 25.29900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.98000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.34950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.98000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.29900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.34950 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 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 VAL A 348 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 MET A 1 CG SD CE REMARK 470 ARG A 4 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 5 CD OE1 OE2 REMARK 470 GLU A 8 CD OE1 OE2 REMARK 470 LYS A 9 CE NZ REMARK 470 ARG A 12 NE CZ NH1 NH2 REMARK 470 GLU A 14 CG CD OE1 OE2 REMARK 470 ARG A 29 CZ NH1 NH2 REMARK 470 LYS A 37 CE NZ REMARK 470 LYS A 80 CD CE NZ REMARK 470 GLU A 143 CD OE1 OE2 REMARK 470 LYS A 188 CD CE NZ REMARK 470 LYS A 242 CE NZ REMARK 470 LYS A 309 CD CE NZ REMARK 470 LYS A 315 CG CD CE NZ REMARK 470 LYS A 333 CD CE NZ REMARK 470 ARG A 336 CD NE CZ NH1 NH2 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 627 O HOH A 716 1.82 REMARK 500 O HOH A 612 O HOH A 699 2.10 REMARK 500 O HOH A 593 O HOH A 847 2.12 REMARK 500 O HOH A 578 O HOH A 811 2.13 REMARK 500 O HOH A 741 O HOH A 816 2.15 REMARK 500 O HOH A 685 O HOH A 865 2.16 REMARK 500 O HOH A 867 O HOH A 868 2.19 REMARK 500 OE1 GLU A 125 O HOH A 713 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 ASN A 78 43.13 -90.91 REMARK 500 GLU A 110 80.10 -67.76 REMARK 500 GLU A 161 -57.73 84.65 REMARK 500 THR A 175 -156.68 -139.97 REMARK 500 ALA A 196 -152.69 -115.11 REMARK 500 ASP A 235 36.02 -98.03 REMARK 500 ASN A 288 17.55 -145.17 REMARK 500 GLN A 304 77.24 -113.28 REMARK 500 ILE A 310 164.38 -45.89 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 A 746 DISTANCE = 5.28 ANGSTROMS REMARK 525 HOH A 778 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A 780 DISTANCE = 5.09 ANGSTROMS REMARK 525 HOH A 781 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 852 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 862 DISTANCE = 6.30 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1N7 A 404 REMARK 610 1N7 A 405 REMARK 610 1N7 A 406 REMARK 610 1N7 A 407 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 401 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 63 SG REMARK 620 2 SF4 A 401 S1 115.2 REMARK 620 3 SF4 A 401 S2 120.4 107.0 REMARK 620 4 SF4 A 401 S4 104.4 103.5 104.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 70 SG REMARK 620 2 SF4 A 401 S1 118.0 REMARK 620 3 SF4 A 401 S2 106.6 108.6 REMARK 620 4 SF4 A 401 S3 113.3 102.3 107.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SAH A 402 N REMARK 620 2 SF4 A 401 S1 85.9 REMARK 620 3 SF4 A 401 S3 150.7 103.1 REMARK 620 4 SF4 A 401 S4 103.2 102.4 102.0 REMARK 620 5 SAH A 402 OXT 69.4 153.5 94.6 93.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 408 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 319 SG REMARK 620 2 CYS A 311 SG 107.9 REMARK 620 3 H2S A 410 S 104.7 117.1 REMARK 620 4 H2S A 409 S 109.3 102.4 115.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 401 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 67 SG REMARK 620 2 SF4 A 401 S2 108.8 REMARK 620 3 SF4 A 401 S3 118.7 107.6 REMARK 620 4 SF4 A 401 S4 115.7 102.8 101.9 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 SF4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1N7 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1N7 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1N7 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1N7 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE H2S A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE H2S A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BR A 414 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IIX RELATED DB: PDB REMARK 900 INTERMEDIATE IN THE TIME COURSE OF FE4S4 CLUSTER REMARK 900 DEGRADATION UPON OXYGEN EXPOSURE REMARK 900 RELATED ID: 3CIW RELATED DB: PDB REMARK 900 INTERMEDIATE IN THE TIME COURSE OF FE4S4 CLUSTER REMARK 900 DEGRADATION UPON OXYGEN EXPOSURE REMARK 900 RELATED ID: 4JXC RELATED DB: PDB REMARK 900 INTERMEDIATE IN THE TIME COURSE OF FE4S4 CLUSTER REMARK 900 DEGRADATION UPON OXYGEN EXPOSURE REMARK 900 RELATED ID: 4JY8 RELATED DB: PDB REMARK 900 INTERMEDIATE IN THE TIME COURSE OF FE4S4 CLUSTER REMARK 900 DEGRADATION UPON OXYGEN EXPOSURE REMARK 900 RELATED ID: 4JY9 RELATED DB: PDB REMARK 900 INTERMEDIATE IN THE TIME COURSE OF FE4S4 CLUSTER REMARK 900 DEGRADATION UPON OXYGEN EXPOSURE REMARK 900 RELATED ID: 4JYF RELATED DB: PDB REMARK 900 RELATED ID: 4JYE RELATED DB: PDB DBREF 4JYD A 1 348 UNP Q9X0Z6 Q9X0Z6_THEMA 1 348 SEQRES 1 A 348 MET THR GLY ARG GLU ILE LEU GLU LYS LEU GLU ARG ARG SEQRES 2 A 348 GLU PHE THR ARG GLU VAL LEU LYS GLU ALA LEU SER ILE SEQRES 3 A 348 ASN ASP ARG GLY PHE ASN GLU ALA LEU PHE LYS LEU ALA SEQRES 4 A 348 ASP GLU ILE ARG ARG LYS TYR VAL GLY ASP GLU VAL HIS SEQRES 5 A 348 ILE ARG ALA ILE ILE GLU PHE SER ASN VAL CYS ARG LYS SEQRES 6 A 348 ASN CYS LEU TYR CYS GLY LEU ARG ARG ASP ASN LYS ASN SEQRES 7 A 348 LEU LYS ARG TYR ARG MET THR PRO GLU GLU ILE VAL GLU SEQRES 8 A 348 ARG ALA ARG LEU ALA VAL GLN PHE GLY ALA LYS THR ILE SEQRES 9 A 348 VAL LEU GLN SER GLY GLU ASP PRO TYR OTY MET PRO ASP SEQRES 10 A 348 VAL ILE SER ASP ILE VAL LYS GLU ILE LYS LYS MET GLY SEQRES 11 A 348 VAL ALA VAL THR LEU SER LEU GLY GLU TRP PRO ARG GLU SEQRES 12 A 348 TYR TYR GLU LYS TRP LYS GLU ALA GLY ALA ASP ARG TYR SEQRES 13 A 348 LEU LEU ARG HIS GLU THR ALA ASN PRO VAL LEU HIS ARG SEQRES 14 A 348 LYS LEU ARG PRO ASP THR SER PHE GLU ASN ARG LEU ASN SEQRES 15 A 348 CYS LEU LEU THR LEU LYS GLU LEU GLY TYR GLU THR GLY SEQRES 16 A 348 ALA GLY SER MET VAL GLY LEU PRO GLY GLN THR ILE ASP SEQRES 17 A 348 ASP LEU VAL ASP ASP LEU LEU PHE LEU LYS GLU HIS ASP SEQRES 18 A 348 PHE ASP MET VAL GLY ILE GLY PRO PHE ILE PRO HIS PRO SEQRES 19 A 348 ASP THR PRO LEU ALA ASN GLU LYS LYS GLY ASP PHE THR SEQRES 20 A 348 LEU THR LEU LYS MET VAL ALA LEU THR ARG ILE LEU LEU SEQRES 21 A 348 PRO ASP SER ASN ILE PRO ALA THR THR ALA MET GLY THR SEQRES 22 A 348 ILE VAL PRO GLY GLY ARG GLU ILE THR LEU ARG CYS GLY SEQRES 23 A 348 ALA ASN VAL ILE MET PRO ASN TRP THR PRO SER PRO TYR SEQRES 24 A 348 ARG GLN LEU TYR GLN LEU TYR PRO GLY LYS ILE CYS VAL SEQRES 25 A 348 PHE GLU LYS ASP THR ALA CYS ILE PRO CYS VAL MET LYS SEQRES 26 A 348 MET ILE GLU LEU LEU GLY ARG LYS PRO GLY ARG ASP TRP SEQRES 27 A 348 GLY GLY ARG LYS ARG VAL PHE GLU THR VAL HET OTY A 114 13 HET SF4 A 401 8 HET SAH A 402 26 HET CPS A 403 42 HET 1N7 A 404 36 HET 1N7 A 405 29 HET 1N7 A 406 25 HET 1N7 A 407 22 HET FE A 408 1 HET H2S A 409 1 HET H2S A 410 1 HET BR A 411 1 HET BR A 412 1 HET BR A 413 1 HET BR A 414 1 HETNAM OTY 2-HYDROXY-L-TYROSINE HETNAM SF4 IRON/SULFUR CLUSTER HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM CPS 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1- HETNAM 2 CPS PROPANESULFONATE HETNAM 1N7 CHAPSO HETNAM FE FE (III) ION HETNAM H2S HYDROSULFURIC ACID HETNAM BR BROMIDE ION HETSYN CPS CHAPS HETSYN 1N7 2-HYDROXY-N,N-DIMETHYL-3-SULFO-N-(3-{[(3BETA,5BETA, HETSYN 2 1N7 7BETA,12BETA)-3,7,12-TRIHYDROXY-24-OXOCHOLAN-24- HETSYN 3 1N7 YL]AMINO}PROPYL)PROPAN-1-AMINIUM HETSYN H2S HYDROGEN SULFIDE FORMUL 1 OTY C9 H11 N O4 FORMUL 2 SF4 FE4 S4 FORMUL 3 SAH C14 H20 N6 O5 S FORMUL 4 CPS C32 H58 N2 O7 S FORMUL 5 1N7 4(C32 H59 N2 O8 S 1+) FORMUL 9 FE FE 3+ FORMUL 10 H2S 2(H2 S) FORMUL 12 BR 4(BR 1-) FORMUL 16 HOH *368(H2 O) HELIX 1 1 THR A 2 ARG A 13 1 12 HELIX 2 2 THR A 16 ILE A 26 1 11 HELIX 3 3 ASP A 28 GLY A 48 1 21 HELIX 4 4 THR A 85 PHE A 99 1 15 HELIX 5 5 ASP A 111 MET A 115 5 5 HELIX 6 6 PRO A 116 LYS A 128 1 13 HELIX 7 7 PRO A 141 ALA A 151 1 11 HELIX 8 8 ASN A 164 ARG A 172 1 9 HELIX 9 9 SER A 176 GLY A 191 1 16 HELIX 10 10 THR A 206 ASP A 221 1 16 HELIX 11 11 ASP A 245 LEU A 260 1 16 HELIX 12 12 THR A 268 VAL A 275 1 8 HELIX 13 13 GLY A 277 ARG A 284 1 8 HELIX 14 14 TYR A 299 TYR A 303 5 5 HELIX 15 15 ALA A 318 LEU A 330 1 13 SHEET 1 A 7 MET A 224 VAL A 225 0 SHEET 2 A 7 GLU A 193 ALA A 196 1 N ALA A 196 O MET A 224 SHEET 3 A 7 ARG A 155 LEU A 157 1 N TYR A 156 O GLU A 193 SHEET 4 A 7 ALA A 132 SER A 136 1 N LEU A 135 O ARG A 155 SHEET 5 A 7 THR A 103 SER A 108 1 N ILE A 104 O THR A 134 SHEET 6 A 7 GLU A 50 SER A 60 1 N ILE A 57 O VAL A 105 SHEET 7 A 7 VAL A 289 ILE A 290 1 O ILE A 290 N HIS A 52 SHEET 1 B 7 MET A 224 VAL A 225 0 SHEET 2 B 7 GLU A 193 ALA A 196 1 N ALA A 196 O MET A 224 SHEET 3 B 7 ARG A 155 LEU A 157 1 N TYR A 156 O GLU A 193 SHEET 4 B 7 ALA A 132 SER A 136 1 N LEU A 135 O ARG A 155 SHEET 5 B 7 THR A 103 SER A 108 1 N ILE A 104 O THR A 134 SHEET 6 B 7 GLU A 50 SER A 60 1 N ILE A 57 O VAL A 105 SHEET 7 B 7 LYS A 333 PRO A 334 1 O LYS A 333 N VAL A 51 SHEET 1 C 2 MET A 199 VAL A 200 0 SHEET 2 C 2 GLY A 228 PRO A 229 1 O GLY A 228 N VAL A 200 LINK SG CYS A 63 FE3 SF4 A 401 1555 1555 2.22 LINK SG CYS A 70 FE4 SF4 A 401 1555 1555 2.26 LINK FE2 SF4 A 401 N SAH A 402 1555 1555 2.28 LINK SG CYS A 319 FE FE A 408 1555 1555 2.31 LINK SG CYS A 67 FE1 SF4 A 401 1555 1555 2.33 LINK SG CYS A 311 FE FE A 408 1555 1555 2.41 LINK C TYR A 113 N OTY A 114 1555 1555 1.33 LINK C OTY A 114 N MET A 115 1555 1555 1.33 LINK FE FE A 408 S H2S A 410 1555 1555 2.26 LINK FE FE A 408 S H2S A 409 1555 1555 2.31 LINK FE2 SF4 A 401 OXT SAH A 402 1555 1555 2.32 CISPEP 1 MET A 115 PRO A 116 0 -8.95 CISPEP 2 SER A 297 PRO A 298 0 5.17 SITE 1 AC1 7 CYS A 63 LYS A 65 CYS A 67 TYR A 69 SITE 2 AC1 7 CYS A 70 GLY A 109 SAH A 402 SITE 1 AC2 19 TYR A 69 GLN A 107 SER A 108 SER A 136 SITE 2 AC2 19 ARG A 159 GLU A 161 ARG A 180 MET A 199 SITE 3 AC2 19 PRO A 229 ILE A 231 TYR A 303 LEU A 305 SITE 4 AC2 19 TYR A 306 SF4 A 401 HOH A 512 HOH A 518 SITE 5 AC2 19 HOH A 520 HOH A 529 HOH A 803 SITE 1 AC3 19 VAL A 97 GLN A 98 PHE A 99 GLY A 100 SITE 2 AC3 19 PRO A 276 GLY A 277 GLU A 280 ARG A 284 SITE 3 AC3 19 MET A 324 LEU A 330 1N7 A 405 1N7 A 406 SITE 4 AC3 19 1N7 A 407 HOH A 509 HOH A 545 HOH A 595 SITE 5 AC3 19 HOH A 605 HOH A 711 HOH A 765 SITE 1 AC4 15 LYS A 37 ASP A 40 LYS A 170 ARG A 284 SITE 2 AC4 15 SER A 297 LYS A 315 ASP A 316 THR A 317 SITE 3 AC4 15 1N7 A 406 HOH A 599 HOH A 642 HOH A 669 SITE 4 AC4 15 HOH A 683 HOH A 688 HOH A 792 SITE 1 AC5 13 ARG A 29 GLU A 33 PHE A 246 THR A 247 SITE 2 AC5 13 LEU A 250 CPS A 403 1N7 A 406 HOH A 594 SITE 3 AC5 13 HOH A 598 HOH A 603 HOH A 787 HOH A 824 SITE 4 AC5 13 HOH A 843 SITE 1 AC6 8 THR A 317 ALA A 318 CPS A 403 1N7 A 404 SITE 2 AC6 8 1N7 A 405 HOH A 627 HOH A 714 HOH A 833 SITE 1 AC7 10 LYS A 128 MET A 324 LYS A 325 GLU A 328 SITE 2 AC7 10 CPS A 403 HOH A 695 HOH A 725 HOH A 755 SITE 3 AC7 10 HOH A 756 HOH A 785 SITE 1 AC8 4 CYS A 311 CYS A 319 H2S A 409 H2S A 410 SITE 1 AC9 4 ARG A 279 CYS A 311 VAL A 323 FE A 408 SITE 1 BC1 3 GLU A 314 CYS A 319 FE A 408 SITE 1 BC2 5 ARG A 64 TRP A 140 PRO A 141 HOH A 567 SITE 2 BC2 5 HOH A 585 SITE 1 BC3 3 ARG A 54 THR A 134 ARG A 155 SITE 1 BC4 4 ARG A 159 PRO A 266 HOH A 638 HOH A 816 SITE 1 BC5 4 ARG A 159 ALA A 270 TYR A 306 HOH A 803 CRYST1 50.598 78.699 85.960 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 0.019764 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011633 0.00000