HEADER OXIDOREDUCTASE 14-FEB-08 3C8Y TITLE 1.39 ANGSTROM CRYSTAL STRUCTURE OF FE-ONLY HYDROGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRON HYDROGENASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: [FE] HYDROGENASE, FE-ONLY HYDROGENASE, CPI; COMPND 5 EC: 1.12.7.2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PASTEURIANUM KEYWDS DITHIOMETHYLETHER, H-CLUSTER, HYDROGENASE, IRON, IRON-SULFUR, METAL- KEYWDS 2 BINDING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.S.PANDEY,B.J.LEMON,J.W.PETERS REVDAT 4 30-AUG-23 3C8Y 1 REMARK LINK REVDAT 3 13-JUL-11 3C8Y 1 VERSN REVDAT 2 24-FEB-09 3C8Y 1 VERSN REVDAT 1 22-APR-08 3C8Y 0 JRNL AUTH A.S.PANDEY,T.V.HARRIS,L.J.GILES,J.W.PETERS,R.K.SZILAGYI JRNL TITL DITHIOMETHYLETHER AS A LIGAND IN THE HYDROGENASE H-CLUSTER. JRNL REF J.AM.CHEM.SOC. V. 130 4533 2008 JRNL REFN ISSN 0002-7863 JRNL PMID 18324814 JRNL DOI 10.1021/JA711187E REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELX REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.140 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5982 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 119840 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.120 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 95779 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4461 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 667 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 46903 REMARK 3 NUMBER OF RESTRAINTS : 55604 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.028 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.051 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.059 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.034 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.003 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.057 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.084 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY 3% REMARK 4 REMARK 4 3C8Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000046490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95364 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 121060 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 46.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.57000 REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1FEH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 4000, 0.1M SODIUM ACETATE (PH REMARK 280 4.6),0.1M SODIUM SULFATE, CAPILLARY DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 55.37500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.37500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.77000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.37500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.37500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.77000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.37500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.37500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.77000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.37500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.37500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 51.77000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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 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 878 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1229 LIES ON A SPECIAL POSITION. 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 840 O HOH A 1110 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN A 12 CA - CB - CG ANGL. DEV. = -13.5 DEGREES REMARK 500 ASP A 42 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 86 NH1 - CZ - NH2 ANGL. DEV. = 9.9 DEGREES REMARK 500 ARG A 86 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 86 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 LEU A 91 CA - CB - CG ANGL. DEV. = 14.6 DEGREES REMARK 500 ARG A 103 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 136 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 144 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ASP A 273 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 305 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 MET A 353 CG - SD - CE ANGL. DEV. = -14.4 DEGREES REMARK 500 ARG A 373 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 373 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 382 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 PHE A 556 CB - CG - CD1 ANGL. DEV. = -4.2 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 LEU A 33 -64.80 -133.71 REMARK 500 ASP A 42 -44.47 -13.14 REMARK 500 THR A 56 -50.25 -132.70 REMARK 500 ASP A 63 22.05 -141.13 REMARK 500 ASN A 75 28.23 -142.79 REMARK 500 ASN A 106 43.14 -154.08 REMARK 500 GLU A 162 14.61 59.96 REMARK 500 SER A 236 -29.22 -141.51 REMARK 500 PHE A 266 -166.34 -110.54 REMARK 500 THR A 334 -72.07 -128.37 REMARK 500 TYR A 445 72.11 -114.02 REMARK 500 TYR A 555 -55.18 -128.08 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 38 -12.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 BOTH LIGAND HCN 575 AND SF4 576 BELONG TO THE SAME HYDROGENASE H- REMARK 600 CLUSTER IN PRIMARY CITATION. 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 580 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 34 SG REMARK 620 2 FES A 580 S1 107.3 REMARK 620 3 FES A 580 S2 122.3 102.9 REMARK 620 4 CYS A 46 SG 95.7 124.8 105.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FES A 580 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 49 SG REMARK 620 2 FES A 580 S1 111.2 REMARK 620 3 FES A 580 S2 113.5 106.3 REMARK 620 4 CYS A 62 SG 101.9 107.7 116.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 579 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 94 NE2 REMARK 620 2 SF4 A 579 S2 108.2 REMARK 620 3 SF4 A 579 S3 124.2 104.9 REMARK 620 4 SF4 A 579 S4 106.4 108.9 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 579 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 98 SG REMARK 620 2 SF4 A 579 S1 112.2 REMARK 620 3 SF4 A 579 S2 115.8 103.3 REMARK 620 4 SF4 A 579 S3 114.4 105.3 104.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 579 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 101 SG REMARK 620 2 SF4 A 579 S1 110.2 REMARK 620 3 SF4 A 579 S3 114.9 105.0 REMARK 620 4 SF4 A 579 S4 114.5 107.1 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 579 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 107 SG REMARK 620 2 SF4 A 579 S1 115.1 REMARK 620 3 SF4 A 579 S2 113.2 103.3 REMARK 620 4 SF4 A 579 S4 111.3 105.3 108.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 578 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 147 SG REMARK 620 2 SF4 A 578 S1 118.8 REMARK 620 3 SF4 A 578 S3 117.7 104.1 REMARK 620 4 SF4 A 578 S4 102.3 104.5 108.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 578 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 150 SG REMARK 620 2 SF4 A 578 S1 118.1 REMARK 620 3 SF4 A 578 S2 101.2 102.6 REMARK 620 4 SF4 A 578 S4 121.1 106.5 104.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 578 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 153 SG REMARK 620 2 SF4 A 578 S2 111.8 REMARK 620 3 SF4 A 578 S3 117.1 103.1 REMARK 620 4 SF4 A 578 S4 112.9 104.0 106.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 577 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 157 SG REMARK 620 2 SF4 A 577 S1 111.8 REMARK 620 3 SF4 A 577 S2 117.7 105.0 REMARK 620 4 SF4 A 577 S4 112.2 105.0 104.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 577 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 190 SG REMARK 620 2 SF4 A 577 S1 120.3 REMARK 620 3 SF4 A 577 S2 119.7 106.9 REMARK 620 4 SF4 A 577 S3 98.4 104.5 104.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 577 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 193 SG REMARK 620 2 SF4 A 577 S2 124.3 REMARK 620 3 SF4 A 577 S3 118.2 101.8 REMARK 620 4 SF4 A 577 S4 103.7 103.7 102.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 577 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 196 SG REMARK 620 2 SF4 A 577 S1 119.7 REMARK 620 3 SF4 A 577 S3 110.6 104.2 REMARK 620 4 SF4 A 577 S4 111.5 105.9 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 578 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 200 SG REMARK 620 2 SF4 A 578 S1 110.4 REMARK 620 3 SF4 A 578 S2 111.1 102.4 REMARK 620 4 SF4 A 578 S3 119.2 106.0 106.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 576 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 SG REMARK 620 2 SF4 A 576 S2 114.7 REMARK 620 3 SF4 A 576 S3 109.4 105.4 REMARK 620 4 SF4 A 576 S4 114.9 107.8 103.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 576 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 355 SG REMARK 620 2 SF4 A 576 S1 105.1 REMARK 620 3 SF4 A 576 S3 110.7 106.3 REMARK 620 4 SF4 A 576 S4 120.8 107.9 105.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 576 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 499 SG REMARK 620 2 SF4 A 576 S1 117.7 REMARK 620 3 SF4 A 576 S2 114.3 104.3 REMARK 620 4 SF4 A 576 S3 108.0 104.8 106.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HCN A 575 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 503 SG REMARK 620 2 HCN A 575 S1 92.3 REMARK 620 3 HCN A 575 C3 93.7 173.8 REMARK 620 4 HCN A 575 C4 92.2 86.8 94.4 REMARK 620 5 HCN A 575 C5 173.8 90.5 83.6 82.5 REMARK 620 6 HCN A 575 S2 94.0 86.5 91.7 171.0 91.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 576 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 503 SG REMARK 620 2 SF4 A 576 S1 119.9 REMARK 620 3 SF4 A 576 S2 118.2 98.9 REMARK 620 4 SF4 A 576 S4 111.3 103.0 103.2 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 HCN A 575 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 576 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 577 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 578 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 579 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FES A 580 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 581 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 582 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 583 DBREF 3C8Y A 1 574 UNP P29166 PHF1_CLOPA 1 574 SEQRES 1 A 574 MET LYS THR ILE ILE ILE ASN GLY VAL GLN PHE ASN THR SEQRES 2 A 574 ASP GLU ASP THR THR ILE LEU LYS PHE ALA ARG ASP ASN SEQRES 3 A 574 ASN ILE ASP ILE SER ALA LEU CYS PHE LEU ASN ASN CYS SEQRES 4 A 574 ASN ASN ASP ILE ASN LYS CYS GLU ILE CYS THR VAL GLU SEQRES 5 A 574 VAL GLU GLY THR GLY LEU VAL THR ALA CYS ASP THR LEU SEQRES 6 A 574 ILE GLU ASP GLY MET ILE ILE ASN THR ASN SER ASP ALA SEQRES 7 A 574 VAL ASN GLU LYS ILE LYS SER ARG ILE SER GLN LEU LEU SEQRES 8 A 574 ASP ILE HIS GLU PHE LYS CYS GLY PRO CYS ASN ARG ARG SEQRES 9 A 574 GLU ASN CYS GLU PHE LEU LYS LEU VAL ILE LYS TYR LYS SEQRES 10 A 574 ALA ARG ALA SER LYS PRO PHE LEU PRO LYS ASP LYS THR SEQRES 11 A 574 GLU TYR VAL ASP GLU ARG SER LYS SER LEU THR VAL ASP SEQRES 12 A 574 ARG THR LYS CYS LEU LEU CYS GLY ARG CYS VAL ASN ALA SEQRES 13 A 574 CYS GLY LYS ASN THR GLU THR TYR ALA MET LYS PHE LEU SEQRES 14 A 574 ASN LYS ASN GLY LYS THR ILE ILE GLY ALA GLU ASP GLU SEQRES 15 A 574 LYS CYS PHE ASP ASP THR ASN CYS LEU LEU CYS GLY GLN SEQRES 16 A 574 CYS ILE ILE ALA CYS PRO VAL ALA ALA LEU SER GLU LYS SEQRES 17 A 574 SER HIS MET ASP ARG VAL LYS ASN ALA LEU ASN ALA PRO SEQRES 18 A 574 GLU LYS HIS VAL ILE VAL ALA MET ALA PRO SER VAL ARG SEQRES 19 A 574 ALA SER ILE GLY GLU LEU PHE ASN MET GLY PHE GLY VAL SEQRES 20 A 574 ASP VAL THR GLY LYS ILE TYR THR ALA LEU ARG GLN LEU SEQRES 21 A 574 GLY PHE ASP LYS ILE PHE ASP ILE ASN PHE GLY ALA ASP SEQRES 22 A 574 MET THR ILE MET GLU GLU ALA THR GLU LEU VAL GLN ARG SEQRES 23 A 574 ILE GLU ASN ASN GLY PRO PHE PRO MET PHE THR SER CYS SEQRES 24 A 574 CYS PRO GLY TRP VAL ARG GLN ALA GLU ASN TYR TYR PRO SEQRES 25 A 574 GLU LEU LEU ASN ASN LEU SER SER ALA LYS SER PRO GLN SEQRES 26 A 574 GLN ILE PHE GLY THR ALA SER LYS THR TYR TYR PRO SER SEQRES 27 A 574 ILE SER GLY LEU ASP PRO LYS ASN VAL PHE THR VAL THR SEQRES 28 A 574 VAL MET PRO CYS THR SER LYS LYS PHE GLU ALA ASP ARG SEQRES 29 A 574 PRO GLN MET GLU LYS ASP GLY LEU ARG ASP ILE ASP ALA SEQRES 30 A 574 VAL ILE THR THR ARG GLU LEU ALA LYS MET ILE LYS ASP SEQRES 31 A 574 ALA LYS ILE PRO PHE ALA LYS LEU GLU ASP SER GLU ALA SEQRES 32 A 574 ASP PRO ALA MET GLY GLU TYR SER GLY ALA GLY ALA ILE SEQRES 33 A 574 PHE GLY ALA THR GLY GLY VAL MET GLU ALA ALA LEU ARG SEQRES 34 A 574 SER ALA LYS ASP PHE ALA GLU ASN ALA GLU LEU GLU ASP SEQRES 35 A 574 ILE GLU TYR LYS GLN VAL ARG GLY LEU ASN GLY ILE LYS SEQRES 36 A 574 GLU ALA GLU VAL GLU ILE ASN ASN ASN LYS TYR ASN VAL SEQRES 37 A 574 ALA VAL ILE ASN GLY ALA SER ASN LEU PHE LYS PHE MET SEQRES 38 A 574 LYS SER GLY MET ILE ASN GLU LYS GLN TYR HIS PHE ILE SEQRES 39 A 574 GLU VAL MET ALA CYS HIS GLY GLY CYS VAL ASN GLY GLY SEQRES 40 A 574 GLY GLN PRO HIS VAL ASN PRO LYS ASP LEU GLU LYS VAL SEQRES 41 A 574 ASP ILE LYS LYS VAL ARG ALA SER VAL LEU TYR ASN GLN SEQRES 42 A 574 ASP GLU HIS LEU SER LYS ARG LYS SER HIS GLU ASN THR SEQRES 43 A 574 ALA LEU VAL LYS MET TYR GLN ASN TYR PHE GLY LYS PRO SEQRES 44 A 574 GLY GLU GLY ARG ALA HIS GLU ILE LEU HIS PHE LYS TYR SEQRES 45 A 574 LYS LYS HET HCN A 575 18 HET SF4 A 576 8 HET SF4 A 577 8 HET SF4 A 578 8 HET SF4 A 579 8 HET FES A 580 4 HET GOL A 581 6 HET GOL A 582 6 HET GOL A 583 6 HETNAM HCN 2 IRON/2 SULFUR/3 CARBONYL/2 CYANIDE/WATER/METHYLETHER HETNAM 2 HCN CLUSTER HETNAM SF4 IRON/SULFUR CLUSTER HETNAM FES FE2/S2 (INORGANIC) CLUSTER HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 HCN C7 H10 FE2 N2 O5 S2 FORMUL 3 SF4 4(FE4 S4) FORMUL 7 FES FE2 S2 FORMUL 8 GOL 3(C3 H8 O3) FORMUL 11 HOH *667(H2 O) HELIX 1 1 THR A 18 ASN A 26 1 9 HELIX 2 2 CYS A 62 THR A 64 5 3 HELIX 3 3 SER A 76 ASP A 92 1 17 HELIX 4 4 CYS A 107 LYS A 117 1 11 HELIX 5 5 ASP A 128 GLU A 131 5 4 HELIX 6 6 THR A 145 CYS A 147 5 3 HELIX 7 7 GLY A 151 GLU A 162 1 12 HELIX 8 8 ALA A 179 LYS A 183 5 5 HELIX 9 9 CYS A 184 THR A 188 5 5 HELIX 10 10 GLY A 194 CYS A 200 1 7 HELIX 11 11 HIS A 210 ALA A 220 1 11 HELIX 12 12 PRO A 231 ASN A 242 5 12 HELIX 13 13 VAL A 249 GLY A 261 1 13 HELIX 14 14 ILE A 268 ASN A 290 1 23 HELIX 15 15 CYS A 300 TYR A 311 1 12 HELIX 16 16 PRO A 312 LEU A 318 5 7 HELIX 17 17 SER A 323 LYS A 333 1 11 HELIX 18 18 THR A 334 ILE A 339 1 6 HELIX 19 19 ASP A 343 LYS A 345 5 3 HELIX 20 20 THR A 356 ASP A 363 1 8 HELIX 21 21 THR A 381 ALA A 391 1 11 HELIX 22 22 PRO A 394 LEU A 398 5 5 HELIX 23 23 ASP A 404 GLY A 408 5 5 HELIX 24 24 SER A 411 ILE A 416 1 6 HELIX 25 25 GLY A 421 ASN A 437 1 17 HELIX 26 26 TYR A 445 ARG A 449 5 5 HELIX 27 27 GLY A 473 SER A 483 1 11 HELIX 28 28 GLY A 484 GLU A 488 5 5 HELIX 29 29 GLY A 502 GLY A 506 5 5 HELIX 30 30 ASN A 513 VAL A 520 1 8 HELIX 31 31 ASP A 521 LEU A 537 1 17 HELIX 32 32 LYS A 541 GLU A 544 5 4 HELIX 33 33 ASN A 545 TYR A 555 1 11 HELIX 34 34 GLU A 561 LEU A 568 1 8 SHEET 1 A 5 VAL A 9 THR A 13 0 SHEET 2 A 5 LYS A 2 ILE A 6 -1 N ILE A 4 O PHE A 11 SHEET 3 A 5 ILE A 71 ASN A 73 1 O ILE A 72 N ILE A 5 SHEET 4 A 5 THR A 50 VAL A 53 -1 N GLU A 52 O ASN A 73 SHEET 5 A 5 GLY A 57 THR A 60 -1 O GLY A 57 N VAL A 53 SHEET 1 B 3 VAL A 133 ASP A 134 0 SHEET 2 B 3 LEU A 140 ASP A 143 -1 O VAL A 142 N ASP A 134 SHEET 3 B 3 LEU A 205 GLU A 207 -1 O SER A 206 N THR A 141 SHEET 1 C 2 LYS A 167 LYS A 171 0 SHEET 2 C 2 LYS A 174 GLY A 178 -1 O LYS A 174 N LYS A 171 SHEET 1 D 4 LYS A 264 ASP A 267 0 SHEET 2 D 4 HIS A 224 MET A 229 1 N VAL A 227 O PHE A 266 SHEET 3 D 4 VAL A 347 MET A 353 1 O PHE A 348 N HIS A 224 SHEET 4 D 4 ALA A 377 THR A 380 1 O ILE A 379 N THR A 351 SHEET 1 E 4 MET A 295 PHE A 296 0 SHEET 2 E 4 PHE A 493 MET A 497 1 O ILE A 494 N MET A 295 SHEET 3 E 4 ASN A 464 ASN A 472 1 N ILE A 471 O GLU A 495 SHEET 4 E 4 ILE A 454 ILE A 461 -1 N ILE A 461 O ASN A 464 SHEET 1 F 2 GLU A 368 LYS A 369 0 SHEET 2 F 2 LEU A 372 ARG A 373 -1 O LEU A 372 N LYS A 369 LINK SG CYS A 34 FE2 AFES A 580 1555 1555 2.32 LINK SG ACYS A 46 FE2 AFES A 580 1555 1555 2.04 LINK SG ACYS A 49 FE1 AFES A 580 1555 1555 2.33 LINK SG ACYS A 62 FE1 AFES A 580 1555 1555 2.34 LINK NE2AHIS A 94 FE1 ASF4 A 579 1555 1555 2.06 LINK SG ACYS A 98 FE4 ASF4 A 579 1555 1555 2.28 LINK SG ACYS A 101 FE2 ASF4 A 579 1555 1555 2.30 LINK SG ACYS A 107 FE3 ASF4 A 579 1555 1555 2.31 LINK SG ACYS A 147 FE2 ASF4 A 578 1555 1555 2.39 LINK SG ACYS A 150 FE3 ASF4 A 578 1555 1555 2.31 LINK SG ACYS A 153 FE1 ASF4 A 578 1555 1555 2.34 LINK SG ACYS A 157 FE3 ASF4 A 577 1555 1555 2.27 LINK SG ACYS A 190 FE4 ASF4 A 577 1555 1555 2.30 LINK SG ACYS A 193 FE1 ASF4 A 577 1555 1555 2.30 LINK SG ACYS A 196 FE2 ASF4 A 577 1555 1555 2.31 LINK SG ACYS A 200 FE4 ASF4 A 578 1555 1555 2.30 LINK SG ACYS A 300 FE1 ASF4 A 576 1555 1555 2.27 LINK SG ACYS A 355 FE2 ASF4 A 576 1555 1555 2.30 LINK SG ACYS A 499 FE4 ASF4 A 576 1555 1555 2.30 LINK SG ACYS A 503 FE1 AHCN A 575 1555 1555 2.39 LINK SG ACYS A 503 FE3 ASF4 A 576 1555 1555 2.28 CISPEP 1 GLY A 291 PRO A 292 0 1.93 CISPEP 2 PHE A 293 PRO A 294 0 -9.13 SITE 1 AC1 15 ALA A 230 PRO A 231 SER A 232 ILE A 268 SITE 2 AC1 15 ALA A 272 CYS A 299 PRO A 324 GLN A 325 SITE 3 AC1 15 MET A 353 PRO A 354 CYS A 355 LYS A 358 SITE 4 AC1 15 PHE A 417 MET A 497 CYS A 503 SITE 1 AC2 6 CYS A 300 PRO A 301 CYS A 355 CYS A 499 SITE 2 AC2 6 CYS A 503 GLY A 506 SITE 1 AC3 9 CYS A 157 THR A 163 MET A 166 CYS A 190 SITE 2 AC3 9 LEU A 191 LEU A 192 CYS A 193 GLY A 194 SITE 3 AC3 9 CYS A 196 SITE 1 AC4 10 CYS A 147 LEU A 148 LEU A 149 CYS A 150 SITE 2 AC4 10 GLY A 151 CYS A 153 CYS A 200 PRO A 201 SITE 3 AC4 10 ALA A 204 LEU A 205 SITE 1 AC5 9 HIS A 94 GLU A 95 PHE A 96 LYS A 97 SITE 2 AC5 9 CYS A 98 CYS A 101 CYS A 107 LYS A 146 SITE 3 AC5 9 ALA A 203 SITE 1 AC6 7 LEU A 33 CYS A 34 PHE A 35 CYS A 46 SITE 2 AC6 7 GLU A 47 CYS A 49 CYS A 62 SITE 1 AC7 7 LYS A 223 LYS A 333 LYS A 345 PHE A 348 SITE 2 AC7 7 ARG A 373 ASP A 376 HOH A1087 SITE 1 AC8 8 ARG A 104 ASN A 106 CYS A 107 LEU A 110 SITE 2 AC8 8 LYS A 111 ASN A 437 HOH A 795 HOH A1008 SITE 1 AC9 5 LYS A 223 PHE A 348 HOH A 701 HOH A 846 SITE 2 AC9 5 HOH A 855 CRYST1 110.750 110.750 103.540 90.00 90.00 90.00 P 42 21 2 8 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 0.009029 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009658 0.00000