HEADER ELECTRON TRANSPORT 03-AUG-00 1FI9 TITLE SOLUTION STRUCTURE OF THE IMIDAZOLE COMPLEX OF CYTOCHROME C COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EQUUS CABALLUS; SOURCE 3 ORGANISM_COMMON: HORSE; SOURCE 4 ORGANISM_TAXID: 9796; SOURCE 5 TISSUE: HEART KEYWDS CYTOCHROME C, SOLUTION STRUCTURE, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 35 AUTHOR L.BANCI,I.BERTINI,G.LIU,J.LU,T.REDDIG,W.TANG,Y.WU,D.ZHU REVDAT 5 23-FEB-22 1FI9 1 REMARK LINK REVDAT 4 24-FEB-09 1FI9 1 VERSN REVDAT 3 01-APR-03 1FI9 1 JRNL REVDAT 2 13-SEP-00 1FI9 1 DBREF REVDAT 1 23-AUG-00 1FI9 0 JRNL AUTH L.BANCI,I.BERTINI,G.LIU,J.LU,T.REDDIG,W.TANG,Y.WU,D.ZHU JRNL TITL EFFECTS OF EXTRINSIC IMIDAZOLE LIGATION ON THE MOLECULAR AND JRNL TITL 2 ELECTRONIC STRUCTURE OF CYTOCHROME C JRNL REF J.BIOL.INORG.CHEM. V. 6 628 2001 JRNL REFN ISSN 0949-8257 JRNL PMID 11472026 JRNL DOI 10.1007/S007750100240 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 5.0, AMBER 5.0, PSEUDOREM 5.0 REMARK 3 AUTHORS : WUTHRICH ET AL (DYANA), PEARLMAN, CASE, CALDWELL, REMARK 3 ROSS, CHEATHAM, FERGUSON, SEIBEL, SINGH, WEINER, REMARK 3 KOLLMAN (AMBER), BANCI, BERTINI, GORI SAVELLINI, REMARK 3 ROMAGNOLI, TURANO, CREMONINI, LUCHINAT,GARY REMARK 3 (PSEUDOREM) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: OTHER REFINEMENT REMARKS: DYNAMICS REMARK 3 SIMULATED ANNEALING,RESTRAINED ENERGY MINIMIZATION; REMARK 3 PSEUDOCONTACT SHIFTS WERE USED IN THE CALCULATION AND IN THE REMARK 3 MINIMIZATION AS FURTHER NON-CLASSICAL CONSTRAINTS REMARK 4 REMARK 4 1FI9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-00. REMARK 100 THE DEPOSITION ID IS D_1000011615. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 5.7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 6MM CYTOCHROME C, 1.2M REMARK 210 IMIDAZOLE; 6MM CYTOCHROME C, REMARK 210 1.2M IMIDAZOLE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PSEUDODYANA 5.0 REMARK 210 METHOD USED : AMBER REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 35 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL 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 32 VAL A 20 CA - CB - CG2 ANGL. DEV. = 9.1 DEGREES REMARK 500 34 LEU A 32 CB - CG - CD2 ANGL. DEV. = 14.0 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 1 CYS A 14 -68.18 -108.79 REMARK 500 1 ALA A 15 -78.29 33.44 REMARK 500 1 CYS A 17 -44.53 -161.38 REMARK 500 1 LYS A 25 -164.59 59.55 REMARK 500 1 LYS A 27 -81.80 -78.53 REMARK 500 1 THR A 28 -60.69 -126.08 REMARK 500 1 LEU A 32 39.82 -78.65 REMARK 500 1 PHE A 36 81.16 -68.03 REMARK 500 1 LYS A 60 45.31 -162.50 REMARK 500 1 GLU A 61 -67.09 65.95 REMARK 500 1 ASN A 70 57.04 179.42 REMARK 500 1 LYS A 73 -57.35 -129.63 REMARK 500 1 THR A 78 -109.40 -101.46 REMARK 500 1 LYS A 79 -26.20 -140.34 REMARK 500 1 MET A 80 71.09 50.70 REMARK 500 2 CYS A 14 -79.97 -111.31 REMARK 500 2 ALA A 15 -74.14 42.41 REMARK 500 2 GLN A 16 47.16 -78.32 REMARK 500 2 CYS A 17 -43.58 -164.89 REMARK 500 2 LYS A 25 -176.43 59.89 REMARK 500 2 LYS A 27 -70.06 -112.63 REMARK 500 2 THR A 28 -57.26 -122.54 REMARK 500 2 GLN A 42 127.44 -173.85 REMARK 500 2 ASN A 52 48.68 -79.63 REMARK 500 2 LYS A 53 -59.37 -162.60 REMARK 500 2 LYS A 60 44.09 -160.82 REMARK 500 2 GLU A 61 -50.79 68.61 REMARK 500 2 GLU A 62 -74.00 -49.17 REMARK 500 2 GLU A 69 41.88 -80.27 REMARK 500 2 ASN A 70 65.40 160.07 REMARK 500 2 LYS A 73 -54.67 -143.70 REMARK 500 2 LYS A 79 78.49 -115.14 REMARK 500 2 PHE A 82 -65.60 -21.51 REMARK 500 2 LYS A 87 -174.23 -173.39 REMARK 500 3 CYS A 14 -70.53 -114.23 REMARK 500 3 ALA A 15 -79.07 39.69 REMARK 500 3 CYS A 17 -42.61 -159.94 REMARK 500 3 LYS A 25 -179.66 58.38 REMARK 500 3 HIS A 26 -72.67 -89.14 REMARK 500 3 LYS A 27 -167.43 54.82 REMARK 500 3 GLN A 42 59.57 -140.64 REMARK 500 3 ALA A 51 -62.17 -163.00 REMARK 500 3 ILE A 57 -168.84 -116.82 REMARK 500 3 LYS A 60 -50.67 -133.32 REMARK 500 3 GLU A 61 -63.51 173.55 REMARK 500 3 ASN A 70 60.50 166.31 REMARK 500 3 LYS A 73 -62.59 -140.64 REMARK 500 3 THR A 78 -63.21 -123.76 REMARK 500 3 LYS A 79 -44.88 -178.07 REMARK 500 3 MET A 80 111.73 61.20 REMARK 500 REMARK 500 THIS ENTRY HAS 726 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 38 0.08 SIDE CHAIN REMARK 500 2 PHE A 82 0.12 SIDE CHAIN REMARK 500 2 TYR A 97 0.08 SIDE CHAIN REMARK 500 4 TYR A 67 0.17 SIDE CHAIN REMARK 500 4 TYR A 97 0.07 SIDE CHAIN REMARK 500 5 TYR A 67 0.07 SIDE CHAIN REMARK 500 6 TYR A 67 0.11 SIDE CHAIN REMARK 500 6 ARG A 91 0.12 SIDE CHAIN REMARK 500 7 TYR A 67 0.14 SIDE CHAIN REMARK 500 7 ARG A 91 0.10 SIDE CHAIN REMARK 500 8 HIS A 18 0.08 SIDE CHAIN REMARK 500 8 TYR A 67 0.08 SIDE CHAIN REMARK 500 8 TYR A 74 0.09 SIDE CHAIN REMARK 500 9 HIS A 18 0.09 SIDE CHAIN REMARK 500 10 TYR A 67 0.11 SIDE CHAIN REMARK 500 10 ARG A 91 0.08 SIDE CHAIN REMARK 500 10 TYR A 97 0.09 SIDE CHAIN REMARK 500 12 TYR A 67 0.07 SIDE CHAIN REMARK 500 13 TYR A 48 0.07 SIDE CHAIN REMARK 500 14 TYR A 67 0.07 SIDE CHAIN REMARK 500 14 TYR A 97 0.11 SIDE CHAIN REMARK 500 15 TYR A 67 0.08 SIDE CHAIN REMARK 500 17 HIS A 18 0.09 SIDE CHAIN REMARK 500 17 TYR A 74 0.11 SIDE CHAIN REMARK 500 18 TYR A 74 0.15 SIDE CHAIN REMARK 500 20 TYR A 67 0.09 SIDE CHAIN REMARK 500 22 PHE A 46 0.08 SIDE CHAIN REMARK 500 23 TYR A 67 0.19 SIDE CHAIN REMARK 500 24 HIS A 18 0.08 SIDE CHAIN REMARK 500 24 TYR A 67 0.09 SIDE CHAIN REMARK 500 25 PHE A 36 0.09 SIDE CHAIN REMARK 500 25 TYR A 74 0.08 SIDE CHAIN REMARK 500 26 TYR A 48 0.10 SIDE CHAIN REMARK 500 26 TYR A 67 0.12 SIDE CHAIN REMARK 500 27 TYR A 97 0.07 SIDE CHAIN REMARK 500 28 TYR A 67 0.10 SIDE CHAIN REMARK 500 29 TYR A 67 0.10 SIDE CHAIN REMARK 500 29 TYR A 74 0.12 SIDE CHAIN REMARK 500 29 PHE A 82 0.09 SIDE CHAIN REMARK 500 31 TYR A 67 0.13 SIDE CHAIN REMARK 500 32 TYR A 67 0.09 SIDE CHAIN REMARK 500 33 HIS A 18 0.09 SIDE CHAIN REMARK 500 33 TYR A 97 0.06 SIDE CHAIN REMARK 500 34 TYR A 67 0.10 SIDE CHAIN REMARK 500 34 TYR A 97 0.07 SIDE CHAIN 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 110 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 HEC A 110 NA 91.8 REMARK 620 3 HEC A 110 NB 88.6 91.5 REMARK 620 4 HEC A 110 NC 88.1 178.9 89.5 REMARK 620 5 HEC A 110 ND 87.4 89.7 175.9 89.3 REMARK 620 6 IMD A 105 N3 176.2 91.2 93.7 88.8 90.3 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 IMD A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC A 110 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FI7 RELATED DB: PDB REMARK 900 1FI7 IS THE MINIMIZED AVERAGE STRUCTURE. DBREF 1FI9 A 1 104 UNP P00004 CYC_HORSE 1 104 SEQRES 1 A 104 GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE VAL GLN LYS SEQRES 2 A 104 CYS ALA GLN CYS HIS THR VAL GLU LYS GLY GLY LYS HIS SEQRES 3 A 104 LYS THR GLY PRO ASN LEU HIS GLY LEU PHE GLY ARG LYS SEQRES 4 A 104 THR GLY GLN ALA PRO GLY PHE THR TYR THR ASP ALA ASN SEQRES 5 A 104 LYS ASN LYS GLY ILE THR TRP LYS GLU GLU THR LEU MET SEQRES 6 A 104 GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY THR SEQRES 7 A 104 LYS MET ILE PHE ALA GLY ILE LYS LYS LYS THR GLU ARG SEQRES 8 A 104 GLU ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN GLU HET IMD A 105 9 HET HEC A 110 75 HETNAM IMD IMIDAZOLE HETNAM HEC HEME C FORMUL 2 IMD C3 H5 N2 1+ FORMUL 3 HEC C34 H34 FE N4 O4 HELIX 1 1 ASP A 2 CYS A 14 1 13 HELIX 2 2 THR A 49 GLY A 56 1 8 HELIX 3 3 THR A 63 LEU A 68 1 6 HELIX 4 4 LYS A 87 ASN A 103 1 17 LINK SG CYS A 14 CAB HEC A 110 1555 1555 1.83 LINK SG CYS A 17 CAC HEC A 110 1555 1555 1.81 LINK NE2 HIS A 18 FE HEC A 110 1555 1555 1.94 LINK N3 IMD A 105 FE HEC A 110 1555 1555 1.97 SITE 1 AC1 3 TYR A 67 LYS A 79 HEC A 110 SITE 1 AC2 17 LYS A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC2 17 THR A 28 GLY A 29 PRO A 30 LEU A 32 SITE 3 AC2 17 LEU A 35 THR A 49 ASN A 52 TRP A 59 SITE 4 AC2 17 TYR A 67 LEU A 68 LYS A 79 LEU A 94 SITE 5 AC2 17 IMD A 105 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1