HEADER ELECTRON TRANSPORT 10-AUG-05 2AMS TITLE STRUCTURE OF THE OXIDIZED HIPIP FROM THERMOCHROMATIUM TEPIDUM AT 1.4 TITLE 2 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH POTENTIAL IRON-SULFUR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIPIP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALLOCHROMATIUM VINOSUM; SOURCE 3 ORGANISM_TAXID: 1049; SOURCE 4 GENE: HIP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IRON-SULFUR PROTEIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR L.M.HUNSICKER-WANG,W.HAN,C.D.STOUT,L.NOODLEMAN,J.A.FEE REVDAT 6 23-AUG-23 2AMS 1 REMARK REVDAT 5 09-SEP-20 2AMS 1 TITLE REMARK LINK REVDAT 4 11-OCT-17 2AMS 1 REMARK REVDAT 3 13-JUL-11 2AMS 1 VERSN REVDAT 2 24-FEB-09 2AMS 1 VERSN REVDAT 1 15-AUG-06 2AMS 0 JRNL AUTH L.M.HUNSICKER-WANG,W.HAN,C.D.STOUT,L.NOODLEMAN,J.A.FEE JRNL TITL GEOMETRIC FACTORS DETERMINE, IN PART, THE ELECTRONIC STATE JRNL TITL 2 OF THE 4FE-4S CLUSTER OF HIPIP FROM THERMOCHROMTIUM TEPIDUM: JRNL TITL 3 A GEOMTERIC, CRYSTALLOGRAPHIC, AND THEORETICAL STUDY. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.4 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) : 0.157 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.157 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) : 2197 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 11710 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.150 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)) : 9761 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 616 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 78 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 : 3008 REMARK 3 NUMBER OF RESTRAINTS : 0 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 2.200 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL 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 1% REMARK 4 REMARK 4 2AMS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000034076. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : D*TREK 8.0SSI REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11907 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 36.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 200 DATA REDUNDANCY : 4.650 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 14.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1IUA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM CITRATE, REMARK 280 NACL, PH 3.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 11.73000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.52500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.27500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.52500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 11.73000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.27500 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 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: 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 ASP A 10 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 TYR A 19 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 28 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 28 NE - CZ - NH2 ANGL. DEV. = -3.8 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 LYS A 25 48.77 -107.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 AUTHOR STATES THAT THE OXIDATION STATE OF THE 4FE-4S REMARK 600 CLUSTER IS TO BE VERIFIED. 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 84 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 43 SG REMARK 620 2 SF4 A 84 S2 116.1 REMARK 620 3 SF4 A 84 S3 113.9 103.5 REMARK 620 4 SF4 A 84 S4 114.2 104.6 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 84 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 46 SG REMARK 620 2 SF4 A 84 S1 113.8 REMARK 620 3 SF4 A 84 S2 115.4 104.8 REMARK 620 4 SF4 A 84 S3 111.8 105.4 104.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 84 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 61 SG REMARK 620 2 SF4 A 84 S1 104.9 REMARK 620 3 SF4 A 84 S3 118.8 103.3 REMARK 620 4 SF4 A 84 S4 118.0 105.8 104.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 84 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 75 SG REMARK 620 2 SF4 A 84 S1 105.9 REMARK 620 3 SF4 A 84 S2 127.0 101.6 REMARK 620 4 SF4 A 84 S4 110.2 106.2 104.2 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 SO4 A 85 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 86 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 84 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 87 DBREF 2AMS A 1 83 UNP P80176 HIP_THETI 1 83 SEQRES 1 A 83 ALA ALA PRO ALA ASN ALA VAL THR ALA ASP ASP PRO THR SEQRES 2 A 83 ALA ILE ALA LEU LYS TYR ASN GLN ASP ALA THR LYS SER SEQRES 3 A 83 GLU ARG VAL ALA ALA ALA ARG PRO GLY LEU PRO PRO GLU SEQRES 4 A 83 GLU GLN HIS CYS ALA ASN CYS GLN PHE MET GLN ALA ASN SEQRES 5 A 83 VAL GLY GLU GLY ASP TRP LYS GLY CYS GLN LEU PHE PRO SEQRES 6 A 83 GLY LYS LEU ILE ASN VAL ASN GLY TRP CYS ALA SER TRP SEQRES 7 A 83 THR LEU LYS ALA GLY HET SO4 A 85 5 HET SO4 A 86 5 HET SF4 A 84 8 HET GOL A 87 6 HETNAM SO4 SULFATE ION HETNAM SF4 IRON/SULFUR CLUSTER HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 SF4 FE4 S4 FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *78(H2 O) HELIX 1 1 ASP A 11 LEU A 17 1 7 HELIX 2 2 ASP A 22 SER A 26 5 5 HELIX 3 3 GLU A 27 ALA A 32 1 6 HELIX 4 4 PRO A 37 GLN A 41 5 5 HELIX 5 5 HIS A 42 CYS A 46 5 5 SHEET 1 A 3 MET A 49 GLU A 55 0 SHEET 2 A 3 TRP A 58 CYS A 61 -1 O GLY A 60 N GLN A 50 SHEET 3 A 3 ILE A 69 ASN A 70 -1 O ILE A 69 N LYS A 59 LINK SG CYS A 43 FE1 SF4 A 84 1555 1555 2.21 LINK SG CYS A 46 FE4 SF4 A 84 1555 1555 2.26 LINK SG CYS A 61 FE2 SF4 A 84 1555 1555 2.24 LINK SG CYS A 75 FE3 SF4 A 84 1555 1555 2.24 SITE 1 AC1 6 ALA A 6 VAL A 7 THR A 8 ASP A 11 SITE 2 AC1 6 LYS A 67 HOH A 118 SITE 1 AC2 4 LYS A 18 GLU A 55 GLY A 56 LYS A 59 SITE 1 AC3 6 TYR A 19 CYS A 43 CYS A 46 CYS A 61 SITE 2 AC3 6 LEU A 63 CYS A 75 SITE 1 AC4 5 LYS A 18 GLU A 27 ASN A 45 GLN A 62 SITE 2 AC4 5 HOH A 151 CRYST1 23.460 46.550 59.050 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 0.042626 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021482 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016935 0.00000