PDB Short entry for 2N9J HEADER ELECTRON TRANSPORT 24-NOV-15 2N9J TITLE SOLUTION STRUCTURE OF OXIDIZED HUMAN CYTOCHROME C COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CYCS, CYC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET21 KEYWDS CYTOCHROME C, ELECTRON TRANSFER, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.IMAI,T.SAIO,H.KUMETA,T.UCHIDA,F.INAGAKI,K.ISHIMORI REVDAT 2 14-JUN-23 2N9J 1 REMARK LINK REVDAT 1 17-FEB-16 2N9J 0 JRNL AUTH M.IMAI,T.SAIO,H.KUMETA,T.UCHIDA,F.INAGAKI,K.ISHIMORI JRNL TITL INVESTIGATION OF THE REDOX-DEPENDENT MODULATION OF STRUCTURE JRNL TITL 2 AND DYNAMICS IN HUMAN CYTOCHROME C. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 469 978 2016 JRNL REFN ISSN 0006-291X JRNL PMID 26718409 JRNL DOI 10.1016/J.BBRC.2015.12.079 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ, SPARKY, CYANA REMARK 3 AUTHORS : VARIAN (VNMRJ), GODDARD (SPARKY), GUNTERT, REMARK 3 MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N9J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000104592. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-1 MM [U-99% 13C; U-99% 15N] REMARK 210 CYT C-1, 50 MM SODIUM PHOSPHATE- REMARK 210 2, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D CBCA(CO)NH; 3D REMARK 210 C(CO)NH; 3D HNCO; 3D HNCA; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D HN(CO) REMARK 210 CA; 3D HN(CA)HA; 3D HCCH-TOCSY REMARK 210 ALIPHATIC; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC; 3D HCCH-TOCSY REMARK 210 AROMATIC; HBCBCGCDHD; REMARK 210 HBCBCGCDCEHE REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, TALOS+, SPARKY, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: 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 GLN A 16 47.22 38.92 REMARK 500 1 CYS A 17 -50.23 -137.79 REMARK 500 1 VAL A 20 -47.66 -136.45 REMARK 500 1 LYS A 27 -103.53 -123.43 REMARK 500 1 LEU A 35 -73.99 -41.70 REMARK 500 1 PHE A 36 103.02 -59.80 REMARK 500 1 ASN A 70 83.91 -163.06 REMARK 500 1 LYS A 86 -67.79 -90.88 REMARK 500 2 ILE A 11 -70.56 -81.66 REMARK 500 2 MET A 12 -31.36 -39.38 REMARK 500 2 SER A 15 -86.03 -82.07 REMARK 500 2 GLN A 16 59.21 -112.90 REMARK 500 2 CYS A 17 -50.49 -131.93 REMARK 500 2 VAL A 20 -51.25 -138.20 REMARK 500 2 GLU A 21 114.33 -38.91 REMARK 500 2 LYS A 27 -99.46 -117.64 REMARK 500 2 LEU A 35 -74.61 -40.48 REMARK 500 2 PHE A 36 95.56 -63.83 REMARK 500 2 LYS A 39 177.68 -52.58 REMARK 500 2 ALA A 43 99.85 -39.44 REMARK 500 2 ASN A 52 -62.37 -90.58 REMARK 500 2 ASN A 70 85.60 -167.23 REMARK 500 2 MET A 80 88.84 -52.94 REMARK 500 2 LYS A 87 109.15 -56.61 REMARK 500 3 CYS A 17 -49.76 -140.15 REMARK 500 3 LYS A 27 -175.24 -53.53 REMARK 500 3 THR A 28 -31.54 -38.83 REMARK 500 3 LYS A 39 -171.18 -55.10 REMARK 500 3 ALA A 43 99.90 -39.52 REMARK 500 3 THR A 49 179.37 -52.86 REMARK 500 3 ASN A 70 87.30 -165.71 REMARK 500 3 THR A 78 168.71 -47.04 REMARK 500 3 LYS A 86 -73.81 -110.28 REMARK 500 4 CYS A 17 -57.73 -133.18 REMARK 500 4 VAL A 20 27.33 49.26 REMARK 500 4 LYS A 27 -175.02 -53.27 REMARK 500 4 THR A 28 -29.96 -38.79 REMARK 500 4 HIS A 33 -71.46 -111.55 REMARK 500 4 ALA A 43 99.97 -39.59 REMARK 500 4 ASN A 70 82.50 -164.52 REMARK 500 4 THR A 78 164.32 -44.08 REMARK 500 4 ILE A 81 74.50 -118.33 REMARK 500 4 LYS A 86 -75.77 -95.07 REMARK 500 4 GLU A 90 -38.46 -38.65 REMARK 500 4 ASN A 103 -50.67 -124.07 REMARK 500 5 LYS A 7 -72.94 -72.91 REMARK 500 5 ILE A 11 -70.24 -82.83 REMARK 500 5 CYS A 17 -61.55 -136.87 REMARK 500 5 LYS A 27 -174.36 -53.93 REMARK 500 5 THR A 28 -30.91 -39.33 REMARK 500 REMARK 500 THIS ENTRY HAS 222 RAMACHANDRAN OUTLIERS. 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 500 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 HEC A 500 NA 98.8 REMARK 620 3 HEC A 500 NB 91.4 90.5 REMARK 620 4 HEC A 500 NC 85.2 174.8 92.7 REMARK 620 5 HEC A 500 ND 88.6 89.0 179.5 87.8 REMARK 620 6 MET A 80 SD 167.6 91.0 96.1 84.6 83.9 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 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25908 RELATED DB: BMRB REMARK 900 RELATED ID: 2N9I RELATED DB: PDB DBREF 2N9J A 1 104 UNP P99999 CYC_HUMAN 2 105 SEQRES 1 A 104 GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE ILE MET LYS SEQRES 2 A 104 CYS SER 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 TYR SER TYR THR ALA ALA ASN SEQRES 5 A 104 LYS ASN LYS GLY ILE ILE TRP GLY GLU ASP 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 VAL GLY ILE LYS LYS LYS GLU GLU ARG SEQRES 8 A 104 ALA ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN GLU HET HEC A 500 75 HETNAM HEC HEME C FORMUL 2 HEC C34 H34 FE N4 O4 HELIX 1 1 VAL A 3 CYS A 14 1 12 HELIX 2 2 ASP A 62 ASN A 70 1 9 HELIX 3 3 ASN A 70 ILE A 75 1 6 HELIX 4 4 LYS A 88 GLU A 104 1 17 LINK SG CYS A 14 CAB HEC A 500 1555 1555 1.80 LINK SG CYS A 17 CAC HEC A 500 1555 1555 1.86 LINK NE2 HIS A 18 FE HEC A 500 1555 1555 1.82 LINK SD MET A 80 FE HEC A 500 1555 1555 2.27 SITE 1 AC1 16 LYS A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC1 16 THR A 28 PRO A 30 THR A 40 GLY A 41 SITE 3 AC1 16 TYR A 48 ASN A 52 TRP A 59 TYR A 67 SITE 4 AC1 16 THR A 78 LYS A 79 MET A 80 LEU A 98 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