HEADER ELECTRON TRANSPORT 01-MAR-02 1IUA TITLE ULTRA-HIGH RESOLUTION STRUCTURE OF HIPIP FROM THERMOCHROMATIUM TEPIDUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH-POTENTIAL IRON-SULFUR PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCHROMATIUM TEPIDUM; SOURCE 3 ORGANISM_TAXID: 1050 KEYWDS HIPIP, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR L.LIU,T.NOGI,M.KOBAYASHI,T.NOZAWA,K.MIKI REVDAT 6 27-DEC-23 1IUA 1 REMARK REVDAT 5 23-JAN-19 1IUA 1 ATOM REVDAT 4 24-FEB-09 1IUA 1 VERSN REVDAT 3 07-JAN-03 1IUA 1 REMARK REVDAT 2 10-JUL-02 1IUA 1 JRNL REVDAT 1 20-MAR-02 1IUA 0 JRNL AUTH L.LIU,T.NOGI,M.KOBAYASHI,T.NOZAWA,K.MIKI JRNL TITL ULTRAHIGH-RESOLUTION STRUCTURE OF HIGH-POTENTIAL IRON-SULFUR JRNL TITL 2 PROTEIN FROM THERMOCHROMATIUM TEPIDUM. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 58 1085 2002 JRNL REFN ISSN 0907-4449 JRNL PMID 12077426 JRNL DOI 10.1107/S0907444902006261 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.NOGI,I.FATHIR,M.KOBAYASHI,T.NOZAWA,K.MIKI REMARK 1 TITL CRYSTAL STRUCTURES OF PHOTOSYNTHETIC REACTION CENTER AND REMARK 1 TITL 2 HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM THERMOCHROMATIUM REMARK 1 TITL 3 TEPIDUM: THERMOSTABILITY AND ELECTRON TRANSFER REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 97 13561 2000 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.240224997 REMARK 1 REFERENCE 2 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. 0.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.101 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.092 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.114 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2842 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 60959 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL 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)) : 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 : 23 REMARK 3 SOLVENT ATOMS : 93 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 : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL 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: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NO RESTRAINT FOR THE LAST FULL-MATRIX REMARK 3 REFINEMENT REMARK 4 REMARK 4 1IUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1000005283. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAR-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL40B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7293 REMARK 200 MONOCHROMATOR : UNDULATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64373 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 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) : 0.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7M A/S, 0.05M SODIUM CITRATE, PH REMARK 280 3.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.2K 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 22.34850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 11.72700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.13600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 11.72700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.34850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.13600 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 27 O HOH A 6090 4455 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 116.0 105.4 REMARK 620 4 SF4 A 84 S4 112.7 104.6 104.2 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 114.3 REMARK 620 3 SF4 A 84 S3 115.4 104.6 REMARK 620 4 SF4 A 84 S4 112.1 105.2 104.3 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 104.7 REMARK 620 3 SF4 A 84 S2 119.0 105.4 REMARK 620 4 SF4 A 84 S4 117.8 104.8 103.6 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 104.8 REMARK 620 3 SF4 A 84 S2 109.3 106.4 REMARK 620 4 SF4 A 84 S3 126.6 103.5 104.6 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 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SF4 A 84 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EYT RELATED DB: PDB REMARK 900 1EYT CONTAINS THE SAME PROTEIN AT 1.5 A STRUCTURE DBREF 1IUA 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 901 5 HET SO4 A 902 5 HET SO4 A 903 5 HET SF4 A 84 8 HETNAM SO4 SULFATE ION HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 SF4 FE4 S4 FORMUL 6 HOH *93(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 2.25 LINK SG CYS A 46 FE2 SF4 A 84 1555 1555 2.27 LINK SG CYS A 61 FE3 SF4 A 84 1555 1555 2.26 LINK SG CYS A 75 FE4 SF4 A 84 1555 1555 2.26 SITE 1 AC1 11 LYS A 18 GLU A 27 GLY A 54 GLU A 55 SITE 2 AC1 11 GLY A 56 LYS A 59 HOH A6020 HOH A6026 SITE 3 AC1 11 HOH A6053 HOH A6082 HOH A6091 SITE 1 AC2 6 ALA A 1 VAL A 7 THR A 8 ASP A 11 SITE 2 AC2 6 LYS A 25 LYS A 67 SITE 1 AC3 6 GLN A 50 ALA A 51 ASN A 52 HOH A6035 SITE 2 AC3 6 HOH A6058 HOH A6088 SITE 1 AC4 7 TYR A 19 CYS A 43 CYS A 46 MET A 49 SITE 2 AC4 7 CYS A 61 LEU A 63 CYS A 75 CRYST1 44.697 58.272 23.454 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 0.022373 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.042637 0.00000