HEADER ELECTRON TRANSPORT 15-APR-09 3H31 TITLE STRUCTURE OF RHODOTHERMUS MARINUS HIPIP AT 1.0 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIGH POTENTIAL IRON-SULFUR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 54-127; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOTHERMUS MARINUS; SOURCE 3 ORGANISM_TAXID: 29549; SOURCE 4 STRAIN: ITI-378; SOURCE 5 GENE: HIP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-GOLD(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET12A KEYWDS IRON-SULFUR PROTEIN, ELECTRON TRANSPORT, IRON, METAL-BINDING, KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.STELTER,A.M.P.MELO,L.SARAIVA,M.TEIXEIRA,M.ARCHER REVDAT 4 13-NOV-24 3H31 1 REMARK REVDAT 3 24-JAN-18 3H31 1 REMARK REVDAT 2 24-AUG-11 3H31 1 JRNL VERSN REVDAT 1 15-DEC-09 3H31 0 JRNL AUTH M.STELTER,A.M.P.MELO,G.O.HREGGVIDSSON,S.HJORLEIFSDOTTIR, JRNL AUTH 2 L.M.SARAIVA,M.TEIXEIRA,M.ARCHER JRNL TITL STRUCTURE AT 1.0 A RESOLUTION OF A HIGH-POTENTIAL JRNL TITL 2 IRON-SULFUR PROTEIN INVOLVED IN THE AEROBIC RESPIRATORY JRNL TITL 3 CHAIN OF RHODOTHERMUS MARINUS JRNL REF J.BIOL.INORG.CHEM. V. 15 303 2010 JRNL REFN ISSN 0949-8257 JRNL PMID 20225399 JRNL DOI 10.1007/S00775-009-0603-8 REMARK 2 REMARK 2 RESOLUTION. 1.00 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : 0.104 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.104 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.144 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 521 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 55765 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.085 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)) : 42735 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 563 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 690.59 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 482.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 18 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7289 REMARK 3 NUMBER OF RESTRAINTS : 9514 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.042 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.033 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.120 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.111 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.053 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.007 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.051 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.095 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: NULL REMARK 4 REMARK 4 3H31 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000052628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JAN-07; 06-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : SLS; ROTATING ANODE REMARK 200 BEAMLINE : X06SA; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918; 1.541 REMARK 200 MONOCHROMATOR : SI 111; MIRRORS REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD; REMARK 200 MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30715 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 46.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : 0.12800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.39600 REMARK 200 R SYM FOR SHELL (I) : 0.39600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, DIOXANE, SODIUM REMARK 280 CITRATE, PH 4, 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 13.63350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.39350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.67150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.39350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.63350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.67150 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 THR A 74 C THR A 74 O -0.222 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 ALA A 1 CB - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 GLU A 2 OE1 - CD - OE2 ANGL. DEV. = 13.1 DEGREES REMARK 500 ARG A 19 N - CA - CB ANGL. DEV. = -18.8 DEGREES REMARK 500 ARG A 19 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 TYR A 30 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ASP A 32 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ASP A 32 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ALA A 73 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 THR A 74 N - CA - CB ANGL. DEV. = 13.1 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 TRP A 69 127.62 -38.49 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 ALA A 1 -13.77 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 75 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 35 SG REMARK 620 2 SF4 A 75 S1 116.2 REMARK 620 3 SF4 A 75 S3 111.9 104.9 REMARK 620 4 SF4 A 75 S4 113.8 105.4 103.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 75 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 38 SG REMARK 620 2 SF4 A 75 S1 115.3 REMARK 620 3 SF4 A 75 S2 115.6 104.4 REMARK 620 4 SF4 A 75 S3 110.4 104.4 105.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 75 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 53 SG REMARK 620 2 SF4 A 75 S2 103.7 REMARK 620 3 SF4 A 75 S3 116.6 105.3 REMARK 620 4 SF4 A 75 S4 120.2 106.9 103.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 75 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 66 SG REMARK 620 2 SF4 A 75 S1 125.9 REMARK 620 3 SF4 A 75 S2 106.1 103.6 REMARK 620 4 SF4 A 75 S4 108.6 104.1 107.2 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 SF4 A 75 REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY REMARK 999 EXIST. DBREF 3H31 A 1 74 UNP C4P582 C4P582_RHOMR 54 127 SEQRES 1 A 74 ALA GLU LEU THR CYS THR ASP VAL SER GLY LEU THR ALA SEQRES 2 A 74 GLU GLU ILE GLN MET ARG GLU SER LEU GLN TYR THR ASP SEQRES 3 A 74 HIS SER PRO TYR PRO ASP LYS THR CYS ALA ASN CYS GLN SEQRES 4 A 74 LEU TYR VAL PRO ALA GLU SER PRO ASP GLN CYS GLY GLY SEQRES 5 A 74 CYS GLN LEU ILE LYS GLY PRO ILE HIS PRO ASN GLY TYR SEQRES 6 A 74 CYS THR SER TRP VAL GLN LYS ALA THR HET SF4 A 75 8 HETNAM SF4 IRON/SULFUR CLUSTER FORMUL 2 SF4 FE4 S4 FORMUL 3 HOH *140(H2 O) HELIX 1 1 THR A 12 LEU A 22 1 11 HELIX 2 2 THR A 34 CYS A 38 5 5 SHEET 1 A 2 TYR A 41 VAL A 42 0 SHEET 2 A 2 GLY A 52 CYS A 53 -1 O GLY A 52 N VAL A 42 SSBOND 1 CYS A 5 CYS A 50 1555 1555 2.03 LINK SG CYS A 35 FE2 SF4 A 75 1555 1555 2.26 LINK SG CYS A 38 FE4 SF4 A 75 1555 1555 2.27 LINK SG CYS A 53 FE1 SF4 A 75 1555 1555 2.26 LINK SG CYS A 66 FE3 SF4 A 75 1555 1555 2.27 SITE 1 AC1 6 CYS A 35 CYS A 38 TYR A 41 CYS A 53 SITE 2 AC1 6 ILE A 56 CYS A 66 CRYST1 27.267 43.343 46.787 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 0.036674 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023072 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021373 0.00000