HEADER ELECTRON TRANSPORT 21-JAN-99 1B7C OBSLTE 22-MAR-00 1B7C 1C75 TITLE 0.97 A CRYSTAL STRUCTURE OF CYTOCHROME C-553 FROM BACILLUS TITLE 2 PASTEURII COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C-553; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: COMPLEXED WITH PROTOPORPHYRIN IX CONTAINING COMPND 5 FE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS PASTEURII; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 STRAIN: DSM 33; SOURCE 5 COLLECTION: DSM 33; SOURCE 6 CELLULAR_LOCATION: CYTOPLASM; SOURCE 7 OTHER_DETAILS: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN (DSM) KEYWDS C-553, HEME, CYTOCHROME, BACILLUS PASTEURII, CYTOCHROME C- KEYWDS 2 553 EXPDTA X-RAY DIFFRACTION AUTHOR S.BENINI,S.CIURLI,W.R.RYPNIEWSKI,K.S.WILSON REVDAT 2 22-MAR-00 1B7C 1 OBSLTE REVDAT 1 21-JAN-00 1B7C 0 JRNL AUTH S.BENINI,M.BORSARI,S.CIURLI,A.DIKIY,M.LAMBORGHINI JRNL TITL MODULATION OF BACILLUS PASTEURII CYTOCHROME C553 JRNL TITL 2 REDUCTION POTENTIAL BY STRUCTURAL AND SOLUTION JRNL TITL 3 PARAMETERS JRNL REF J.BIOL.INORG.CHEM. V. 3 371 1998 JRNL REFN ASTM JJBCFA GW ISSN 0949-8257 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.BENINI,S.CIURLI,W.R.RYPNIEWSKI,K.S.WILSON REMARK 1 TITL CRYSTALS OF CYTOCHROME C-553 FROM BACILLUS REMARK 1 TITL 2 PASTEURII SHOW DIFFRACTION TO 0.97 A RESOLUTION REMARK 1 REF PROTEINS: STRUCT., FUNCT., V. 28 580 1997 REMARK 1 REF 2 GENET. REMARK 1 REFN ASTM PSFGEY US ISSN 0887-3585 REMARK 2 REMARK 2 RESOLUTION. 0.97 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) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.116 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.116 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 38898 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.112 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.112 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)) : 35419 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 986 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 120 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 661.12 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 486.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 14 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6286 REMARK 3 NUMBER OF RESTRAINTS : 7877 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.034 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.020 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.034 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.117 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.095 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.064 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.048 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.117 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201 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 1B7C COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-1999. REMARK 100 THE RCSB ID CODE IS RCSB000342. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-1996 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8855 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : SEGMENTED MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38959 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.970 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.460 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : 7.40000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.1600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.72 REMARK 200 R MERGE FOR SHELL (I) : 0.24200 REMARK 200 R SYM FOR SHELL (I) : 24.20000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.180 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: REFMAC ARP (CCP4) REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2 M AMMONIUM SULPHATE IN 100 MM REMARK 280 SODIUM CITRATE BUFFER PH 5.0 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 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 18.57200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.01050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.71100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 22.01050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.57200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.71100 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O HOH 79 O HOH 152 2.15 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ALA A 5 CA - C - N ANGL. DEV. = 17.7 DEGREES REMARK 500 LYS A 29 CB - CG - CD ANGL. DEV. = 17.7 DEGREES SEQRES 1 A 71 VAL ASP ALA GLU ALA VAL VAL GLN GLN LYS CYS ILE SER SEQRES 2 A 71 CYS HIS GLY GLY ASP LEU THR GLY ALA SER ALA PRO ALA SEQRES 3 A 71 ILE ASP LYS ALA GLY ALA ASN TYR SER GLU GLU GLU ILE SEQRES 4 A 71 LEU ASP ILE ILE LEU ASN GLY GLN GLY GLY MET PRO GLY SEQRES 5 A 71 GLY ILE ALA LYS GLY ALA GLU ALA GLU ALA VAL ALA ALA SEQRES 6 A 71 TRP LEU ALA GLU LYS LYS HET HEM A 72 77 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *120(H2 O1) HELIX 1 1 ALA A 3 LYS A 10 1 8 HELIX 2 2 ILE A 12 HIS A 15 1 4 HELIX 3 3 ALA A 30 ALA A 32 5 3 HELIX 4 4 GLU A 36 ASN A 45 1 10 HELIX 5 5 GLY A 57 GLU A 69 1 13 LINK FE HEM A 72 NE2 HIS A 15 CRYST1 37.144 39.422 44.021 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 0.026922 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025366 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022716 0.00000