HEADER OXIDOREDUCTASE 10-JAN-00 1DT1 TITLE THERMUS THERMOPHILUS CYTOCHROME C552 SYNTHESIZED BY ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C552; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYTOCHROME C552, THERMUS THERMOPHILUS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.FEE,Y.CHEN,M.J.HILL,E.GOMEZ-MORAN,T.LOEHR,J.AI,L.THONY-MEYER, AUTHOR 2 P.A.WILLIAMS,E.STURA,V.SRIDHAR,D.E.MCREE REVDAT 8 03-MAR-21 1DT1 1 COMPND REMARK HET HETNAM REVDAT 8 2 1 HETSYN FORMUL LINK ATOM REVDAT 7 31-JAN-18 1DT1 1 REMARK REVDAT 6 13-JUL-11 1DT1 1 VERSN REVDAT 5 24-FEB-09 1DT1 1 VERSN REVDAT 4 01-APR-03 1DT1 1 JRNL REVDAT 3 28-MAR-01 1DT1 1 JRNL REVDAT 2 10-JAN-01 1DT1 1 REMARK REVDAT 1 18-FEB-00 1DT1 0 JRNL AUTH J.A.FEE,Y.CHEN,T.R.TODARO,K.L.BREN,K.M.PATEL,M.G.HILL, JRNL AUTH 2 E.GOMEZ-MORAN,T.M.LOEHR,J.AI,L.THONY-MEYER,P.A.WILLIAMS, JRNL AUTH 3 E.STURA,V.SRIDHAR,D.E.MCREE JRNL TITL INTEGRITY OF THERMUS THERMOPHILUS CYTOCHROME C552 JRNL TITL 2 SYNTHESIZED BY ESCHERICHIA COLI CELLS EXPRESSING THE JRNL TITL 3 HOST-SPECIFIC CYTOCHROME C MATURATION GENES, CCMABCDEFGH: JRNL TITL 4 BIOCHEMICAL, SPECTRAL, AND STRUCTURAL CHARACTERIZATION OF JRNL TITL 5 THE RECOMBINANT PROTEIN. JRNL REF PROTEIN SCI. V. 9 2074 2000 JRNL REFN ISSN 0961-8368 JRNL PMID 11152119 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 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) : 0.204 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.210 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 544 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 10978 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 : 984 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 71 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 AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DT1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1000010341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XFIT, MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15100 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.30400 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: XFIT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 36% MPEG 5K (W/V), 0.2M IM-MAT 6.3, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 24K, PH 6.3, REMARK 280 TEMPERATURE 297.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.23333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 10.61667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.92500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 5.30833 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.54167 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 300 REMARK: THE BIOLOGICAL UNIT IS A MONOMER REMARK 300 AS FOUND IN THE ASYMMETRIC UNIT 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 LYS A 131 C LYS A 131 OXT 0.167 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 GLN A 16 156.51 78.64 REMARK 500 ASN A 66 53.29 -149.43 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 HEC A 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 15 NE2 REMARK 620 2 HEC A 200 NA 91.3 REMARK 620 3 HEC A 200 NB 90.9 91.1 REMARK 620 4 HEC A 200 NC 92.1 176.4 90.1 REMARK 620 5 HEC A 200 ND 92.5 90.7 176.1 87.9 REMARK 620 6 MET A 69 SD 171.9 80.7 90.5 96.0 86.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 200 DBREF 1DT1 A 3 131 UNP Q5SME3 Q5SME3_THET8 20 148 SEQRES 1 A 129 ASP GLY ALA LYS ILE TYR ALA GLN CYS ALA GLY CYS HIS SEQRES 2 A 129 GLN GLN ASN GLY GLN GLY ILE PRO GLY ALA PHE PRO PRO SEQRES 3 A 129 LEU ALA GLY HIS VAL ALA GLU ILE LEU ALA LYS GLU GLY SEQRES 4 A 129 GLY ARG GLU TYR LEU ILE LEU VAL LEU LEU TYR GLY LEU SEQRES 5 A 129 GLN GLY GLN ILE GLU VAL LYS GLY MET LYS TYR ASN GLY SEQRES 6 A 129 VAL MET SER SER PHE ALA GLN LEU LYS ASP GLU GLU ILE SEQRES 7 A 129 ALA ALA VAL LEU ASN HIS ILE ALA THR ALA TRP GLY ASP SEQRES 8 A 129 ALA LYS LYS VAL LYS GLY PHE LYS PRO PHE THR ALA GLU SEQRES 9 A 129 GLU VAL LYS LYS LEU ARG ALA LYS LYS LEU THR PRO GLN SEQRES 10 A 129 GLN VAL LEU ALA GLU ARG LYS LYS LEU GLY LEU LYS HET HEC A 200 43 HETNAM HEC HEME C FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 HOH *71(H2 O) HELIX 1 1 ASP A 3 GLN A 16 1 14 HELIX 2 2 HIS A 32 ALA A 38 1 7 HELIX 3 3 GLY A 41 GLY A 53 1 13 HELIX 4 4 LYS A 76 ALA A 90 1 15 HELIX 5 5 GLY A 92 VAL A 97 5 6 HELIX 6 6 THR A 104 ALA A 113 1 10 HELIX 7 7 THR A 117 LEU A 128 1 12 SHEET 1 A 2 LEU A 54 GLN A 55 0 SHEET 2 A 2 VAL A 68 MET A 69 -1 N MET A 69 O LEU A 54 SHEET 1 B 2 ILE A 58 VAL A 60 0 SHEET 2 B 2 MET A 63 TYR A 65 -1 O MET A 63 N VAL A 60 LINK SG CYS A 11 CAB HEC A 200 1555 1555 1.81 LINK SG CYS A 14 CAC HEC A 200 1555 1555 1.84 LINK NE2 HIS A 15 FE HEC A 200 1555 1555 2.01 LINK SD MET A 69 FE HEC A 200 1555 1555 2.30 SITE 1 AC1 18 GLN A 10 CYS A 11 CYS A 14 HIS A 15 SITE 2 AC1 18 ALA A 25 PRO A 27 HIS A 32 TYR A 45 SITE 3 AC1 18 LEU A 46 GLN A 55 GLY A 56 VAL A 60 SITE 4 AC1 18 GLY A 67 VAL A 68 MET A 69 PHE A 72 SITE 5 AC1 18 GLU A 106 ARG A 125 CRYST1 86.900 86.900 31.850 90.00 90.00 120.00 P 65 6 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 0.011507 0.006644 0.000000 0.00000 SCALE2 0.000000 0.013288 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031397 0.00000