10 20 30 40 50 60 70 80 1YTC - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ELECTRON TRANSPORT 03-JUL-95 1YTC
TITLE THERMODYNAMIC CYCLES AS PROBES OF STRUCTURE-FUNCTION TITLE 2 RELATIONSHIPS IN UNFOLDED PROTEINS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: YEAST ISO-2 CYTOCHROME C; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: REDUCED STATE OF HEME
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS ELECTRON TRANSPORT, HEME PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.LUO,G.D.BRAYER
REVDAT 2 24-FEB-09 1YTC 1 VERSN REVDAT 1 08-MAR-96 1YTC 0
JRNL AUTH W.A.MCGEE,F.I.ROSELL,J.R.LIGGINS, JRNL AUTH 2 S.RODRIGUEZ-GHIDARPOUR,Y.LUO,J.CHEN,G.D.BRAYER, JRNL AUTH 3 A.G.MAUK,B.T.NALL JRNL TITL THERMODYNAMIC CYCLES AS PROBES OF STRUCTURE IN JRNL TITL 2 UNFOLDED PROTEINS. JRNL REF BIOCHEMISTRY V. 35 1995 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8639684 JRNL DOI 10.1021/BI951228F
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.E.P.MURPHY,J.S.FETROW,R.E.BURTON,G.D.BRAYER REMARK 1 TITL THE STRUCTURE AND FUNCTION OF OMEGA LOOP A REMARK 1 TITL 2 REPLACEMENTS IN CYTOCHROME C REMARK 1 REF PROTEIN SCI. V. 2 1429 1993 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.E.P.MURPHY,B.T.NALL,G.D.BRAYER REMARK 1 TITL STRUCTURE DETERMINATION AND ANALYSIS OF YEAST REMARK 1 TITL 2 ISO-2-CYTOCHROME C AND A COMPOSITE MUTANT PROTEIN REMARK 1 REF J.MOL.BIOL. V. 227 160 1992 REMARK 1 REFN ISSN 0022-2836
REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ, X-PLOR 3.1 REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 8985 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 + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.162 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL 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) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 871 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 116 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.00 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) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.937 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.748 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.549 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.308 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1YTC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-92 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS (MSC) REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9141 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 69.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.46000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 18.33000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 18.33000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 104.19000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 18.33000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 18.33000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.73000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 18.33000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 18.33000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 104.19000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 18.33000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 18.33000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.73000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 69.46000 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 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 LYS A -2 N - CA - CB ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG A 13 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 13 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ASP A 50 CB - CG - OD1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ASP A 62 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 TYR A 97 CB - CG - CD2 ANGL. DEV. = -4.9 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 SER A -6 -60.54 -172.87 REMARK 500 LYS A 27 -134.12 -133.38 REMARK 500 ASN A 70 94.73 -163.99 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 HEM A 104 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 MET A 80 SD 172.4 REMARK 620 N 1
REMARK 700 REMARK 700 SHEET REMARK 700 THE PDB HAS GENERATED THE HELIX AND SHEET RECORDS FROM THE REMARK 700 COORDINATES USING A PROGRAM BASED ON DSSP OF W. KABSCH AND REMARK 700 C. SANDER.
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 105 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 104
DBREF 1YTC A -9 103 UNP P00045 CYC7_YEAST 2 113
SEQADV 1YTC ILE A 52 UNP P00045 ASN 62 ENGINEERED
SEQRES 1 A 112 ALA LYS GLU SER THR GLY PHE LYS PRO GLY SER ALA LYS SEQRES 2 A 112 LYS GLY ALA THR LEU PHE LYS THR ARG CYS GLN GLN CYS SEQRES 3 A 112 HIS THR ILE GLU GLU GLY GLY PRO ASN LYS VAL GLY PRO SEQRES 4 A 112 ASN LEU HIS GLY ILE PHE GLY ARG HIS SER GLY GLN VAL SEQRES 5 A 112 LYS GLY TYR SER TYR THR ASP ALA ILE ILE ASN LYS ASN SEQRES 6 A 112 VAL LYS TRP ASP GLU ASP SER MET SER GLU TYR LEU THR SEQRES 7 A 112 ASN PRO M3L LYS TYR ILE PRO GLY THR LYS MET ALA PHE SEQRES 8 A 112 ALA GLY LEU LYS LYS GLU LYS ASP ARG ASN ASP LEU ILE SEQRES 9 A 112 THR TYR MET THR LYS ALA ALA LYS
MODRES 1YTC M3L A 72 LYS N-TRIMETHYLLYSINE
HET M3L A 72 12 HET SO4 A 105 5 HET HEM A 104 43
HETNAM M3L N-TRIMETHYLLYSINE HETNAM SO4 SULFATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE
HETSYN HEM HEME
FORMUL 1 M3L C9 H21 N2 O2 1+ FORMUL 2 SO4 O4 S 2- FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 HOH *116(H2 O)
HELIX 1 1 ALA A 3 ARG A 13 1 11 HELIX 2 2 ILE A 35 GLY A 37 5 3 HELIX 3 3 ASP A 50 LYS A 55 1 6 HELIX 4 4 GLU A 61 THR A 69 1 9 HELIX 5 5 PRO A 71 TYR A 74 1 4 HELIX 6 6 GLU A 88 ALA A 101 1 14
LINK SG CYS A 14 CAB HEM A 104 1555 1555 1.77 LINK SG CYS A 17 CAC HEM A 104 1555 1555 1.82 LINK NE2 HIS A 18 FE HEM A 104 1555 1555 2.04 LINK C PRO A 71 N M3L A 72 1555 1555 1.33 LINK C M3L A 72 N LYS A 73 1555 1555 1.33 LINK FE HEM A 104 SD MET A 80 1555 1555 2.38
SITE 1 AC1 9 SER A 2 ALA A 3 LYS A 4 LYS A 11 SITE 2 AC1 9 SER A 47 LYS A 73 HOH A 123 HOH A 140 SITE 3 AC1 9 HOH A 145 SITE 1 AC2 24 ARG A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC2 24 GLY A 23 VAL A 28 ILE A 35 SER A 40 SITE 3 AC2 24 GLY A 41 TYR A 46 TYR A 48 THR A 49 SITE 4 AC2 24 ILE A 52 TRP A 59 MET A 64 LEU A 68 SITE 5 AC2 24 THR A 78 LYS A 79 MET A 80 ALA A 81 SITE 6 AC2 24 PHE A 82 MET A 98 HOH A 113 HOH A 117
CRYST1 36.660 36.660 138.920 90.00 90.00 90.00 P 43 21 2 8
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 0.027278 0.000000 0.000000 0.00000
SCALE2 0.000000 0.027278 0.000000 0.00000
SCALE3 0.000000 0.000000 0.007198 0.00000