HEADER ELECTRON TRANSPORT 27-APR-98 1C2N TITLE CYTOCHROME C2, NMR, 20 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C2; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOBACTER CAPSULATUS; SOURCE 3 ORGANISM_TAXID: 272942; SOURCE 4 STRAIN: SB1003 KEYWDS ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.CORDIER,M.S.CAFFREY,B.BRUTSCHER,M.A.CUSANOVICH,D.MARION, AUTHOR 2 M.BLACKLEDGE REVDAT 5 30-OCT-24 1C2N 1 REMARK REVDAT 4 05-JUN-24 1C2N 1 REMARK LINK REVDAT 3 13-JUL-11 1C2N 1 VERSN REVDAT 2 24-FEB-09 1C2N 1 VERSN REVDAT 1 23-MAR-99 1C2N 0 JRNL AUTH F.CORDIER,M.CAFFREY,B.BRUTSCHER,M.A.CUSANOVICH,D.MARION, JRNL AUTH 2 M.BLACKLEDGE JRNL TITL SOLUTION STRUCTURE, ROTATIONAL DIFFUSION ANISOTROPY AND JRNL TITL 2 LOCAL BACKBONE DYNAMICS OF RHODOBACTER CAPSULATUS CYTOCHROME JRNL TITL 3 C2. JRNL REF J.MOL.BIOL. V. 281 341 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9698552 JRNL DOI 10.1006/JMBI.1998.1950 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : BIOSYM/MSI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE CALCULATIONS WERE PERFORMED REMARK 3 USING DISCOVER PROGRAMS COMPRISED IN THE INSIGHTII PACKAGE FROM REMARK 3 BIOSYM /MOLECULAR SIMULATIONS. THE AMBER4 FORCE FIELD WAS USED REMARK 3 IN THE RESTRAINED MOLECULAR DYNAMICS REFINEMENT STAGE. FOR REMARK 3 FURTHER DETAILS SEE BLACKLEDGE ET AL. 1995, 245, 661-681. REMARK 4 REMARK 4 1C2N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172166. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 45 MM SODIUM PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; HSQC-NOESY 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 : DISCOVER REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 4 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING HETERONUCLEAR NMR REMARK 210 SPECTROSCOPY. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A -20 REMARK 465 LYS A -19 REMARK 465 ILE A -18 REMARK 465 SER A -17 REMARK 465 LEU A -16 REMARK 465 THR A -15 REMARK 465 ALA A -14 REMARK 465 ALA A -13 REMARK 465 THR A -12 REMARK 465 VAL A -11 REMARK 465 ALA A -10 REMARK 465 ALA A -9 REMARK 465 LEU A -8 REMARK 465 VAL A -7 REMARK 465 LEU A -6 REMARK 465 ALA A -5 REMARK 465 ALA A -4 REMARK 465 PRO A -3 REMARK 465 ALA A -2 REMARK 465 PHE A -1 REMARK 465 ALA A 0 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 4 VAL A 114 CA - CB - CG1 ANGL. DEV. = 10.7 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 ALA A 45 -123.54 36.57 REMARK 500 1 THR A 47 9.13 -160.18 REMARK 500 1 TYR A 53 -176.93 -69.83 REMARK 500 1 ASP A 78 62.63 -151.95 REMARK 500 1 GLU A 85 -70.46 -60.37 REMARK 500 1 LYS A 91 30.18 -80.96 REMARK 500 1 MET A 96 80.78 -68.48 REMARK 500 1 LEU A 100 112.49 -161.05 REMARK 500 1 ALA A 101 33.92 -79.20 REMARK 500 1 VAL A 115 82.73 -64.60 REMARK 500 2 THR A 47 22.94 -145.31 REMARK 500 2 PHE A 51 118.57 -161.31 REMARK 500 2 SER A 63 0.59 -69.56 REMARK 500 2 MET A 96 81.02 -68.26 REMARK 500 2 LYS A 102 139.45 89.30 REMARK 500 3 LYS A 14 5.01 -66.73 REMARK 500 3 PRO A 35 -173.73 -54.69 REMARK 500 3 LEU A 37 6.16 -60.02 REMARK 500 3 TYR A 38 102.44 -59.75 REMARK 500 3 VAL A 41 98.71 -65.06 REMARK 500 3 ALA A 45 -149.86 62.54 REMARK 500 3 THR A 47 21.02 -150.32 REMARK 500 3 MET A 96 78.90 -69.75 REMARK 500 3 ALA A 101 41.44 -80.55 REMARK 500 3 LYS A 102 178.87 179.71 REMARK 500 4 TYR A 38 87.27 -63.43 REMARK 500 4 ASP A 78 73.35 -158.02 REMARK 500 4 MET A 96 79.75 -67.97 REMARK 500 4 ALA A 101 53.32 -114.49 REMARK 500 4 LYS A 102 164.12 75.66 REMARK 500 4 VAL A 114 -81.41 -59.68 REMARK 500 4 VAL A 115 70.87 8.28 REMARK 500 5 ALA A 31 44.22 -84.28 REMARK 500 5 LYS A 32 57.45 13.79 REMARK 500 5 TYR A 38 87.15 -67.55 REMARK 500 5 THR A 44 70.40 -67.40 REMARK 500 5 ALA A 45 -144.91 56.53 REMARK 500 5 ASP A 78 56.79 -159.37 REMARK 500 5 LYS A 91 42.20 -79.53 REMARK 500 5 MET A 96 84.35 -64.96 REMARK 500 5 VAL A 115 94.07 -69.88 REMARK 500 6 ILE A 27 -60.18 -98.62 REMARK 500 6 LYS A 29 70.61 -68.62 REMARK 500 6 ALA A 45 -139.47 53.07 REMARK 500 6 TRP A 67 99.23 -61.01 REMARK 500 6 ASP A 78 49.16 -161.21 REMARK 500 6 MET A 96 82.63 -65.44 REMARK 500 6 ALA A 101 46.72 -79.38 REMARK 500 6 LYS A 102 -165.63 175.59 REMARK 500 6 VAL A 115 82.78 -69.07 REMARK 500 REMARK 500 THIS ENTRY HAS 153 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 ASP A 23 0.09 SIDE CHAIN REMARK 500 1 TYR A 38 0.08 SIDE CHAIN REMARK 500 1 TYR A 48 0.09 SIDE CHAIN REMARK 500 1 PHE A 51 0.12 SIDE CHAIN REMARK 500 1 TYR A 53 0.19 SIDE CHAIN REMARK 500 1 PHE A 65 0.09 SIDE CHAIN REMARK 500 2 GLU A 26 0.07 SIDE CHAIN REMARK 500 2 TYR A 53 0.14 SIDE CHAIN REMARK 500 2 ASP A 106 0.08 SIDE CHAIN REMARK 500 3 ASP A 23 0.09 SIDE CHAIN REMARK 500 3 TYR A 38 0.18 SIDE CHAIN REMARK 500 3 TYR A 53 0.08 SIDE CHAIN REMARK 500 3 GLU A 69 0.10 SIDE CHAIN REMARK 500 4 PHE A 10 0.07 SIDE CHAIN REMARK 500 4 ASP A 23 0.09 SIDE CHAIN REMARK 500 4 GLU A 26 0.07 SIDE CHAIN REMARK 500 4 TYR A 38 0.08 SIDE CHAIN REMARK 500 4 TYR A 48 0.10 SIDE CHAIN REMARK 500 4 PHE A 82 0.13 SIDE CHAIN REMARK 500 5 ASP A 23 0.09 SIDE CHAIN REMARK 500 5 TYR A 38 0.08 SIDE CHAIN REMARK 500 5 TYR A 48 0.07 SIDE CHAIN REMARK 500 5 GLU A 105 0.09 SIDE CHAIN REMARK 500 6 TYR A 48 0.09 SIDE CHAIN REMARK 500 6 TYR A 53 0.11 SIDE CHAIN REMARK 500 6 PHE A 65 0.09 SIDE CHAIN REMARK 500 7 TYR A 48 0.07 SIDE CHAIN REMARK 500 7 PHE A 65 0.09 SIDE CHAIN REMARK 500 7 PHE A 82 0.09 SIDE CHAIN REMARK 500 8 ASP A 23 0.09 SIDE CHAIN REMARK 500 8 PHE A 51 0.08 SIDE CHAIN REMARK 500 9 TYR A 48 0.07 SIDE CHAIN REMARK 500 10 TYR A 38 0.08 SIDE CHAIN REMARK 500 10 ARG A 43 0.10 SIDE CHAIN REMARK 500 10 TYR A 48 0.10 SIDE CHAIN REMARK 500 11 ASP A 23 0.09 SIDE CHAIN REMARK 500 11 TYR A 38 0.12 SIDE CHAIN REMARK 500 11 TYR A 48 0.10 SIDE CHAIN REMARK 500 11 PHE A 51 0.08 SIDE CHAIN REMARK 500 11 GLU A 105 0.08 SIDE CHAIN REMARK 500 12 ASP A 2 0.07 SIDE CHAIN REMARK 500 12 TYR A 48 0.12 SIDE CHAIN REMARK 500 12 PHE A 51 0.12 SIDE CHAIN REMARK 500 12 TYR A 53 0.09 SIDE CHAIN REMARK 500 12 ASP A 106 0.07 SIDE CHAIN REMARK 500 13 PHE A 10 0.12 SIDE CHAIN REMARK 500 13 ASP A 23 0.09 SIDE CHAIN REMARK 500 13 TYR A 75 0.07 SIDE CHAIN REMARK 500 13 ASP A 89 0.09 SIDE CHAIN REMARK 500 14 ASP A 23 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 72 PLANE DEVIATIONS. 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 117 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 17 NE2 REMARK 620 2 HEC A 117 NA 87.0 REMARK 620 3 HEC A 117 NB 89.2 90.1 REMARK 620 4 HEC A 117 NC 92.9 179.8 90.1 REMARK 620 5 HEC A 117 ND 85.1 89.1 174.3 90.7 REMARK 620 6 MET A 96 SD 171.5 101.5 90.4 78.6 95.3 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 HEC A 117 DBREF 1C2N A -20 116 UNP P00094 CYC2_RHOCA 1 137 SEQRES 1 A 137 MET LYS ILE SER LEU THR ALA ALA THR VAL ALA ALA LEU SEQRES 2 A 137 VAL LEU ALA ALA PRO ALA PHE ALA GLY ASP ALA ALA LYS SEQRES 3 A 137 GLY GLU LYS GLU PHE ASN LYS CYS LYS THR CYS HIS SER SEQRES 4 A 137 ILE ILE ALA PRO ASP GLY THR GLU ILE VAL LYS GLY ALA SEQRES 5 A 137 LYS THR GLY PRO ASN LEU TYR GLY VAL VAL GLY ARG THR SEQRES 6 A 137 ALA GLY THR TYR PRO GLU PHE LYS TYR LYS ASP SER ILE SEQRES 7 A 137 VAL ALA LEU GLY ALA SER GLY PHE ALA TRP THR GLU GLU SEQRES 8 A 137 ASP ILE ALA THR TYR VAL LYS ASP PRO GLY ALA PHE LEU SEQRES 9 A 137 LYS GLU LYS LEU ASP ASP LYS LYS ALA LYS THR GLY MET SEQRES 10 A 137 ALA PHE LYS LEU ALA LYS GLY GLY GLU ASP VAL ALA ALA SEQRES 11 A 137 TYR LEU ALA SER VAL VAL LYS HET HEC A 117 75 HETNAM HEC HEME C FORMUL 2 HEC C34 H34 FE N4 O4 HELIX 1 I ALA A 3 GLU A 9 1 7 HELIX 2 II ASP A 55 ALA A 62 1 8 HELIX 3 III GLU A 70 ASP A 78 1 9 HELIX 4 IV ALA A 81 ASP A 88 1 8 HELIX 5 V GLY A 104 VAL A 114 1 11 LINK SG CYS A 13 CAB HEC A 117 1555 1555 1.82 LINK SG CYS A 16 CAC HEC A 117 1555 1555 1.81 LINK NE2 HIS A 17 FE HEC A 117 1555 1555 2.00 LINK SD MET A 96 FE HEC A 117 1555 1555 2.36 SITE 1 AC1 20 LYS A 12 CYS A 13 CYS A 16 HIS A 17 SITE 2 AC1 20 THR A 33 PRO A 35 LEU A 37 ALA A 45 SITE 3 AC1 20 GLY A 46 TYR A 53 LYS A 54 ILE A 57 SITE 4 AC1 20 TRP A 67 TYR A 75 VAL A 76 THR A 94 SITE 5 AC1 20 GLY A 95 MET A 96 PHE A 98 VAL A 107 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