HEADER ELECTRON TRANSPORT 30-JUL-79 156B OBSLTE 15-JAN-91 156B 256B TITLE IMPROVEMENT OF THE 2.5 ANGSTROMS RESOLUTION MODEL OF TITLE 2 CYTOCHROME $B=562= BY REDETERMINING THE PRIMARY STRUCTURE TITLE 3 AND USING MOLECULAR GRAPHICS COMPND MOL_ID: 1; COMPND 2 MOLECULE:; COMPND 3 CHAIN: NULL; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR P.H.BETHGE,E.W.CZERWINSKI,F.S.MATHEWS REVDAT 7 15-JAN-91 156B 3 OBSLTE REVDAT 6 30-SEP-83 156B 1 REVDAT REVDAT 5 16-JUL-81 156B 1 REMARK REVDAT 4 31-DEC-80 156B 1 REMARK REVDAT 3 07-APR-80 156B 3 ATOM HETATM TER REVDAT 2 05-MAR-80 156B 1 SOURCE REVDAT 1 11-SEP-79 156B 0 JRNL AUTH F.LEDERER,A.GLATIGNY,P.H.BETHGE,H.D.BELLAMY, JRNL AUTH 2 F.S.MATHEWS JRNL TITL IMPROVEMENT OF THE 2.5 ANGSTROMS RESOLUTION MODEL JRNL TITL 2 OF CYTOCHROME B=562= BY REDETERMINING THE PRIMARY JRNL TITL 3 STRUCTURE AND USING MOLECULAR GRAPHICS JRNL REF J.MOL.BIOL. V. 148 427 1981 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.S.MATHEWS,P.H.BETHGE,E.W.CZERWINSKI REMARK 1 TITL THE STRUCTURE OF CYTOCHROME B=562= FROM REMARK 1 TITL 2 ESCHERICHIA COLI AT 2.5 ANGSTROMS RESOLUTION REMARK 1 REF J.BIOL.CHEM. V. 254 1699 1979 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.W.CZERWINSKI,F.S.MATHEWS REMARK 1 TITL LOCATION OF THE IRON ATOM AND THE REMARK 1 TITL 2 NON-CRYSTALLOGRAPHIC SYMMETRY ELEMENTS IN REMARK 1 TITL 3 CYTOCHROME B=562= REMARK 1 REF J.MOL.BIOL. V. 86 49 1974 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. NULL ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : NULL REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 802 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 156B COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 156B THE PROTOPORPHYRIN IX IRON ATOM IS COORDINATED TO THE REMARK 5 SIDE 156B CHAINS OF RESIDUES MET 7 AND HIS 106. 156B REMARK 6 REMARK 6 156B CORRECTION. STANDARDIZE FORMAT OF SOURCE RECORD. 156B REMARK 6 05-MAR-80. 156B REMARK 7 REMARK 7 156B CORRECTION. DELETE SPURIOUS ATOM 346 AND RENUMBER ALL REMARK 7 156B FOLLOWING ATOMS. 07-APR-80. 156B REMARK 8 REMARK 8 156B CORRECTION. STANDARDIZE FORMAT OF REMARK 3. 31-DEC-80. REMARK 8 156B REMARK 9 REMARK 9 156B CORRECTION. INSERT NEW PAPER AS REFERENCE 1 AND REMARK 9 RENUMBER 156B OTHERS. THIS NEW PAPER INDICATES THAT THE REMARK 9 PROTEIN HAS 156B BEEN RESEQUENCED SHOWING MAJOR VARIANCE REMARK 9 WITH THE PRESENT 156B SEQUENCE. THE DENSITY MAPS HAVE BEEN REMARK 9 REINTERPRETED IN 156B LIGHT OF THESE CHANGES. THE REMARK 9 COORDINATES AND SEQUENCE IN 156B THIS ENTRY SHOULD BE REMARK 9 TREATED AS PRELIMINARY WITH POSSIBLE 156B ERRORS. NEW REMARK 9 COORDINATES WILL BE DEPOSITED. 16-JUL-81. 156B REMARK 10 REMARK 10 156B CORRECTION. INSERT REVDAT RECORDS. 30-SEP-83. 156B REMARK 11 REMARK 11 156B CORRECTION. THIS ENTRY IS OBSOLETE. 15-JAN-91. 156B REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,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 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN 102 CG OD1 ND2 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 ASP 27 CG2 VAL 31 1.05 REMARK 500 CB PHE 64 CD1 TYR 109 1.21 REMARK 500 CA PHE 64 CE1 TYR 109 1.28 REMARK 500 CB PHE 64 CE1 TYR 109 1.40 REMARK 500 ND2 ASN 26 CB ALA 82 1.43 REMARK 500 O GLN 59 N MET 61 1.47 REMARK 500 O LYS 50 N GLU 52 1.48 REMARK 500 ND2 ASN 26 CA ALA 82 1.51 REMARK 500 OD1 ASP 77 NZ LYS 80 1.59 REMARK 500 N PHE 64 CE1 TYR 109 1.63 REMARK 500 CB ASP 63 OH TYR 109 1.66 REMARK 500 ND2 ASN 26 N ALA 82 1.73 REMARK 500 N PHE 64 OH TYR 109 1.76 REMARK 500 O ASN 26 CG LEU 30 1.78 REMARK 500 CD1 LEU 81 N ALA 90 1.78 REMARK 500 CG ASP 63 OH TYR 109 1.80 REMARK 500 O ASN 26 CB LEU 30 1.81 REMARK 500 AD1 ASX 22 NZ LYS 24 1.85 REMARK 500 CD1 LEU 81 CA ALA 90 1.87 REMARK 500 N PHE 64 CZ TYR 109 1.88 REMARK 500 OD1 ASP 63 OH TYR 109 1.89 REMARK 500 O ALA 103 N HIS 106 1.92 REMARK 500 O LYS 15 N GLU 18 1.93 REMARK 500 O HIS 66 CB ASP 69 2.00 REMARK 500 O ASN 26 CD1 LEU 30 2.01 REMARK 500 C ASP 63 OH TYR 109 2.05 REMARK 500 O HIS 66 N ASP 69 2.08 REMARK 500 OD1 ASP 77 CE LYS 80 2.08 REMARK 500 O GLN 96 N THR 99 2.08 REMARK 500 CG ASN 26 CB ALA 82 2.12 REMARK 500 O ARG 101 CB HIS 106 2.12 REMARK 500 CA PHE 64 CD1 TYR 109 2.13 REMARK 500 O ASN 11 N LEU 14 2.14 REMARK 500 C ASP 27 CG2 VAL 31 2.14 REMARK 500 CA ASP 63 OH TYR 109 2.14 REMARK 500 SD MET 7 FE HEM 1 2.17 REMARK 500 NZ LYS 15 NZ LYS 19 2.18 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP 6 C MET 7 N -0.173 REMARK 500 ASN 41 CA ASN 41 C 0.277 REMARK 500 LYS 98 N LYS 98 CA 0.180 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 VAL 31 N - CA - CB ANGL. DEV. =-26.6 DEGREES REMARK 500 LYS 98 N - CA - CB ANGL. DEV. =-25.6 DEGREES REMARK 500 LYS 98 C - N - CA ANGL. DEV. =-24.9 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 ASX 22 -170.63 134.84 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP 5 ASP 6 -148.38 SEQRES 1 103 ALA ASP LEU GLU ASP ASP MET GLN THR LEU ASN ASP ASN SEQRES 2 103 LEU LYS VAL ILE GLU LYS ALA ASX ASX GLX LYS ALA ASN SEQRES 3 103 ASP ALA ALA LEU VAL LYS MET ARG ALA ALA ALA LEU ASN SEQRES 4 103 ALA GLN LYS ALA THR PRO PRO LYS LEU GLU ASP ASN SER SEQRES 5 103 GLN PRO MET LYS ASP PHE ARG HIS GLY PHE ASP ILE LEU SEQRES 6 103 VAL GLU GLY ILE ASP ASP ALA LEU LYS LEU ALA ASN GLU SEQRES 7 103 GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA GLU GLN LEU SEQRES 8 103 LYS THR THR ARG ASN ALA TYR HIS GLN LYS TYR ARG FTNOTE 1 FOR ASN 102, THE SIDE CHAIN BEYOND CB HAS BEEN OMITTED. HET HEM 1 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 HELIX 1 A ASP 2 LYS 19 1 18 HELIX 2 B LYS 24 LYS 45 1 19 HELIX 3 C LYS 62 GLY 85 1 24 HELIX 4 D LYS 88 LYS 108 1 20 TURN 1 1 LEU 51 ASN 57 RESIDUES 54-56 OMITTED TURN 2 2 GLN 59 LYS 62 CRYST1 33.710 50.480 32.730 102.76 86.55 106.70 P 1 2 ORIGX1 0.029665 0.008900 0.000109 0.00000 ORIGX2 0.000000 0.020682 0.004507 0.00000 ORIGX3 0.000000 0.000000 0.031327 0.00000 SCALE1 0.029665 0.008900 0.000109 0.00000 SCALE2 0.000000 0.020682 0.004507 0.00000 SCALE3 0.000000 0.000000 0.031327 0.00000 MTRIX1 1 -0.053984 0.216100 -0.974864 0.00000 MTRIX2 1 0.216218 -0.950325 -0.222851 0.00000 MTRIX3 1 -0.974406 -0.222618 0.004609 0.00000