HEADER ELECTRON TRANSPORT 08-MAY-00 1EYT TITLE CRYSTAL STRUCTURE OF HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM TITLE 2 THERMOCHROMATIUM TEPIDUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH-POTENTIAL IRON-SULFUR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HIPIP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCHROMATIUM TEPIDUM; SOURCE 3 ORGANISM_TAXID: 1050 KEYWDS IRON-SULFUR PROTEIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR T.NOGI,I.FATHIR,M.KOBAYASHI,T.NOZAWA,K.MIKI REVDAT 4 07-FEB-24 1EYT 1 REMARK LINK REVDAT 3 24-MAR-09 1EYT 1 LINK ATOM CONECT REVDAT 2 24-FEB-09 1EYT 1 VERSN REVDAT 1 13-DEC-00 1EYT 0 JRNL AUTH T.NOGI,I.FATHIR,M.KOBAYASHI,T.NOZAWA,K.MIKI JRNL TITL CRYSTAL STRUCTURES OF PHOTOSYNTHETIC REACTION CENTER AND JRNL TITL 2 HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM THERMOCHROMATIUM JRNL TITL 3 TEPIDUM: THERMOSTABILITY AND ELECTRON TRANSFER. JRNL REF PROC.NATL.ACAD.SCI.USA V. 97 13561 2000 JRNL REFN ISSN 0027-8424 JRNL PMID 11095707 JRNL DOI 10.1073/PNAS.240224997 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.NOGI,M.KOBAYASHI,T.NOZAWA,K.MIKI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC ANALYSIS OF REMARK 1 TITL 2 HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM THERMOCHROMATIUM REMARK 1 TITL 3 TEPIDUM REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 56 656 2000 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444900003127 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 10271 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 508 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL 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 : 8 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.40 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.170 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EYT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-00. REMARK 100 THE DEPOSITION ID IS D_1000011038. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : WEISSENBERG REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9746 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.7 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.21900 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: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM CITRATE, PH REMARK 280 3.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.0K 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 23.55900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 11.81000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.79600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 11.81000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.55900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.79600 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 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 112.8 REMARK 620 3 SF4 A 84 S3 116.9 105.3 REMARK 620 4 SF4 A 84 S4 112.7 105.1 102.9 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 46 SG REMARK 620 2 SF4 A 84 S1 113.3 REMARK 620 3 SF4 A 84 S3 116.1 104.7 REMARK 620 4 SF4 A 84 S4 111.2 106.2 104.6 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 61 SG REMARK 620 2 SF4 A 84 S1 106.1 REMARK 620 3 SF4 A 84 S2 120.3 104.2 REMARK 620 4 SF4 A 84 S4 117.5 103.6 103.2 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 75 SG REMARK 620 2 SF4 A 84 S1 104.1 REMARK 620 3 SF4 A 84 S2 110.4 108.0 REMARK 620 4 SF4 A 84 S3 124.8 103.4 105.1 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 84 DBREF 1EYT 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 SF4 A 84 8 HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 2 SF4 FE4 S4 FORMUL 3 HOH *43(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 ASN A 45 5 4 SHEET 1 A 3 MET A 49 GLU A 55 0 SHEET 2 A 3 TRP A 58 CYS A 61 -1 N TRP A 58 O GLU A 55 SHEET 3 A 3 ILE A 69 ASN A 70 -1 N ILE A 69 O LYS A 59 LINK SG CYS A 43 FE1 SF4 A 84 1555 1555 2.23 LINK SG CYS A 46 FE2 SF4 A 84 1555 1555 2.22 LINK SG CYS A 61 FE3 SF4 A 84 1555 1555 2.20 LINK SG CYS A 75 FE4 SF4 A 84 1555 1555 2.26 SITE 1 AC1 6 TYR A 19 CYS A 43 CYS A 46 CYS A 61 SITE 2 AC1 6 LEU A 63 CYS A 75 CRYST1 47.118 59.592 23.620 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 0.021223 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016781 0.000000 0.00000 SCALE3 0.000000 0.000000 0.042337 0.00000