HEADER OXIDOREDUCTASE 12-SEP-03 1QYZ TITLE CHARACTERIZATION OF THE MALFORMED, RECOMBINANT CYTOCHROME TITLE 2 RC552 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C-552; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: C552; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274; SOURCE 4 GENE: CYCA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MALFORMED CYTOCHROME C, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.FEE,T.R.TODARO,E.LUNA,D.SANDERS,L.M.HUNSICKER-WANG, AUTHOR 2 K.M.PATEL,K.L.BREN,E.GOMEZ-MORAN,M.G.HILL,J.AI,T.M.LOEHR, AUTHOR 3 W.A.OERTLING,P.A.WILLIAMS,C.D.STOUT,D.MCREE,A.PASTUSZYN REVDAT 2 24-FEB-09 1QYZ 1 VERSN REVDAT 1 28-SEP-04 1QYZ 0 JRNL AUTH J.A.FEE,T.R.TODARO,E.LUNA,D.SANDERS, JRNL AUTH 2 L.M.HUNSICKER-WANG,K.M.PATEL,K.L.BREN, JRNL AUTH 3 E.GOMEZ-MORAN,M.G.HILL,J.AI,T.M.LOEHR,W.A.OERTLING, JRNL AUTH 4 P.A.WILLIAMS,C.D.STOUT,D.MCREE,A.PASTUSZYN JRNL TITL CYTOCHROME RC552, FORMED DURING EXPRESSION OF THE JRNL TITL 2 TRUNCATED, THERMUS THERMOPHILUS CYTOCHROME C552 JRNL TITL 3 GENE IN THE CYTOPLASM OF ESCHERICHIA COLI, REACTS JRNL TITL 4 SPONTANEOUSLY TO FORM PROTEIN-BOUND JRNL TITL 5 2-FORMYL-4-VINYL (SPIROGRAPHIS) HEME. JRNL REF BIOCHEMISTRY V. 43 12162 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15379555 JRNL DOI 10.1021/BI048968L REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 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) : 0.205 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.197 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1496 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 27649 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.184 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.178 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1106 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 21193 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 997 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1154.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 3 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10441 REMARK 3 NUMBER OF RESTRAINTS : 12768 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.025 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.024 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.036 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.049 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.018 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.003 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.052 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.068 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: ANISOTROPIC REFINEMENT REDUCED FREE REMARK 3 R (NO CUTOFF) BY 0.9% REMARK 4 REMARK 4 1QYZ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-03. REMARK 100 THE RCSB ID CODE IS RCSB020240. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-02 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 : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92017 REMARK 200 MONOCHROMATOR : FLAT MIRROR (VERTICAL REMARK 200 FOCUSING), SINGLE CRYSTAL REMARK 200 SI(311) BENT MONOCHROMATOR REMARK 200 (HORIZONTAL FOCUSING) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31680 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 2.500 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) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 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: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5K MME, IMIDAZOLE-MALATE REMARK 280 BUFFER, NACL, PH 6.3, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 21.47267 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 10.73633 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 16.10450 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 5.36817 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 26.84083 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 1 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 CYS A 11 CA - C - O ANGL. DEV. = 17.2 DEGREES REMARK 500 CYS A 11 O - C - N ANGL. DEV. = -14.4 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 CYS A 11 26.06 -140.71 REMARK 500 CYS A 14 -60.98 -101.52 REMARK 500 GLN A 16 155.49 81.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1174 DISTANCE = 5.10 ANGSTROMS 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 HCO A 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 15 NE2 REMARK 620 2 MET A 69 SD 174.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HCO A 200 DBREF 1QYZ A 1 131 UNP P04164 C552_THETH 18 148 SEQRES 1 A 131 GLN ALA ASP GLY ALA LYS ILE TYR ALA GLN CYS ALA GLY SEQRES 2 A 131 CYS HIS GLN GLN ASN GLY GLN GLY ILE PRO GLY ALA PHE SEQRES 3 A 131 PRO PRO LEU ALA GLY HIS VAL ALA GLU ILE LEU ALA LYS SEQRES 4 A 131 GLU GLY GLY ARG GLU TYR LEU ILE LEU VAL LEU LEU TYR SEQRES 5 A 131 GLY LEU GLN GLY GLN ILE GLU VAL LYS GLY MET LYS TYR SEQRES 6 A 131 ASN GLY VAL MET SER SER PHE ALA GLN LEU LYS ASP GLU SEQRES 7 A 131 GLU ILE ALA ALA VAL LEU ASN HIS ILE ALA THR ALA TRP SEQRES 8 A 131 GLY ASP ALA LYS LYS VAL LYS GLY PHE LYS PRO PHE THR SEQRES 9 A 131 ALA GLU GLU VAL LYS LYS LEU ARG ALA LYS LYS LEU THR SEQRES 10 A 131 PRO GLN GLN VAL LEU ALA GLU ARG LYS LYS LEU GLY LEU SEQRES 11 A 131 LYS HET HCO A 200 44 HETNAM HCO 2-ACETYL-PROTOPORPHYRIN IX FORMUL 2 HCO C34 H34 FE N4 O5 FORMUL 3 HOH *121(H2 O) HELIX 1 1 ASP A 3 GLN A 10 1 8 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 O MET A 69 N 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 TYR A 65 N ILE A 58 LINK NE2 HIS A 15 FE HCO A 200 1555 1555 2.01 LINK SG CYS A 11 CBB HCO A 200 1555 1555 2.05 LINK SD MET A 69 FE HCO A 200 1555 1555 2.32 LINK SG CYS A 14 CAC HCO A 200 1555 1555 1.86 SITE 1 AC1 17 TYR A 8 CYS A 11 CYS A 14 HIS A 15 SITE 2 AC1 17 PRO A 27 HIS A 32 TYR A 45 LEU A 46 SITE 3 AC1 17 GLN A 55 GLY A 56 VAL A 60 TYR A 65 SITE 4 AC1 17 GLY A 67 VAL A 68 MET A 69 PHE A 72 SITE 5 AC1 17 ARG A 125 CRYST1 87.463 87.463 32.209 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 0.011433 0.006601 0.000000 0.00000 SCALE2 0.000000 0.013202 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031047 0.00000