PDB Short entry for 2L4D HEADER ELECTRON TRANSPORT 04-OCT-10 2L4D TITLE CYTOCHROME C DOMAIN OF PP3183 PROTEIN FROM PSEUDOMONAS PUTIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCO1/SENC FAMILY PROTEIN/CYTOCHROME C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 222-327; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 160488; SOURCE 4 STRAIN: KT2440; SOURCE 5 GENE: PP3183, PP_3183; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PEC86 KEYWDS CYTOCHROME C, SCO, ELECTRON TRANSFER, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.BANCI,I.BERTINI,S.CIOFI-BAFFONI,T.KOZYREVA,M.MORI,S.WANG REVDAT 2 13-APR-11 2L4D 1 JRNL REVDAT 1 26-JAN-11 2L4D 0 JRNL AUTH L.BANCI,I.BERTINI,S.CIOFI-BAFFONI,T.KOZYREVA,M.MORI,S.WANG JRNL TITL SCO PROTEINS ARE INVOLVED IN ELECTRON TRANSFER PROCESSES JRNL REF J.BIOL.INORG.CHEM. V. 16 391 2011 JRNL REFN ISSN 0949-8257 JRNL PMID 21181421 JRNL DOI 10.1007/S00775-010-0735-X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L4D COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-OCT-10. REMARK 100 THE RCSB ID CODE IS RCSB101941. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-100% 15N] CYTOCHROME C REMARK 210 -1, 0.8 MM [U-100% 13C; U-100% REMARK 210 15N] CYTOCHROME C-2, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D HNCA; REMARK 210 3D HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; 2D REMARK 210 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 700 MHZ; 500 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, XEASY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST ENERGY 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 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 PHE A -1 REMARK 465 THR 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 11 ARG A 9 NE - CZ - NH2 ANGL. DEV. = -3.0 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 ARG A 9 35.63 -148.69 REMARK 500 1 CYS A 10 -33.88 -157.95 REMARK 500 1 VAL A 16 74.05 -117.88 REMARK 500 1 GLN A 36 -56.59 -136.40 REMARK 500 1 VAL A 48 43.26 -160.19 REMARK 500 1 TYR A 67 -63.97 -90.41 REMARK 500 1 ASN A 68 16.01 -156.69 REMARK 500 1 THR A 98 54.92 38.97 REMARK 500 1 PRO A 99 32.41 -79.20 REMARK 500 1 THR A 101 19.63 55.45 REMARK 500 1 ASN A 102 80.00 -158.22 REMARK 500 2 CYS A 10 -9.23 -143.13 REMARK 500 2 ASN A 18 32.38 -77.61 REMARK 500 2 VAL A 48 58.72 -141.52 REMARK 500 2 ALA A 71 85.72 59.00 REMARK 500 3 LEU A 30 -12.16 -140.99 REMARK 500 3 ARG A 69 -110.01 61.87 REMARK 500 3 LEU A 70 -151.94 62.18 REMARK 500 3 VAL A 100 -44.77 55.43 REMARK 500 3 ASN A 102 -50.97 59.64 REMARK 500 4 VAL A 16 77.41 -118.56 REMARK 500 4 VAL A 48 58.71 -141.06 REMARK 500 4 TYR A 67 48.19 -92.16 REMARK 500 4 ALA A 80 -2.87 61.19 REMARK 500 4 GLU A 81 -60.06 -99.57 REMARK 500 4 ARG A 103 26.55 49.37 REMARK 500 5 CYS A 13 -59.45 -149.23 REMARK 500 5 TYR A 67 66.83 -110.80 REMARK 500 5 ASN A 68 18.83 59.01 REMARK 500 5 ARG A 69 19.14 51.96 REMARK 500 5 ALA A 71 -165.98 60.61 REMARK 500 5 ASN A 102 -12.95 57.79 REMARK 500 6 CYS A 10 -30.05 -136.15 REMARK 500 6 GLU A 20 70.63 48.06 REMARK 500 6 PRO A 21 -159.75 -72.74 REMARK 500 6 ILE A 26 -27.10 65.89 REMARK 500 6 LYS A 56 77.48 45.57 REMARK 500 6 TYR A 67 46.71 -95.41 REMARK 500 6 ALA A 71 77.77 57.89 REMARK 500 6 MET A 75 -81.56 -73.18 REMARK 500 6 ARG A 76 4.46 -164.88 REMARK 500 6 THR A 101 -58.09 -145.67 REMARK 500 7 CYS A 13 -14.65 -143.40 REMARK 500 7 ASN A 18 -98.07 -141.51 REMARK 500 7 THR A 19 -14.60 55.49 REMARK 500 7 GLN A 23 36.20 -146.36 REMARK 500 7 VAL A 48 45.58 -140.85 REMARK 500 7 LEU A 59 -31.99 61.11 REMARK 500 7 TYR A 67 39.35 -89.38 REMARK 500 7 ALA A 71 134.94 60.52 REMARK 500 REMARK 500 THIS ENTRY HAS 168 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL 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 A 57 PRO A 58 1 -146.95 REMARK 500 LEU A 96 GLN A 97 8 -149.67 REMARK 500 LYS A 56 ASP A 57 12 -144.46 REMARK 500 ILE A 26 GLY A 27 13 144.32 REMARK 500 THR A 98 PRO A 99 17 144.42 REMARK 500 ASP A 57 PRO A 58 20 -149.10 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 1 HEC A 107 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 14 NE2 REMARK 620 2 HEC A 107 NA 93.4 REMARK 620 3 HEC A 107 NB 90.7 90.2 REMARK 620 4 HEC A 107 NC 87.7 178.7 90.6 REMARK 620 5 HEC A 107 ND 89.6 90.1 179.6 89.1 REMARK 620 6 MET A 72 SD 166.9 99.4 86.6 79.5 93.0 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 107 DBREF 2L4D A 1 106 UNP Q88I19 Q88I19_PSEPK 222 327 SEQADV 2L4D GLY A -3 UNP Q88I19 EXPRESSION TAG SEQADV 2L4D SER A -2 UNP Q88I19 EXPRESSION TAG SEQADV 2L4D PHE A -1 UNP Q88I19 EXPRESSION TAG SEQADV 2L4D THR A 0 UNP Q88I19 EXPRESSION TAG SEQRES 1 A 110 GLY SER PHE THR SER GLY GLU GLN ILE PHE ARG THR ARG SEQRES 2 A 110 CYS SER SER CYS HIS THR VAL GLY ASN THR GLU PRO GLY SEQRES 3 A 110 GLN PRO GLY ILE GLY PRO ASP LEU LEU GLY VAL THR ARG SEQRES 4 A 110 GLN ARG ASP ALA ASN TRP LEU VAL ARG TRP LEU LYS VAL SEQRES 5 A 110 PRO ASP GLN MET LEU ALA GLU LYS ASP PRO LEU ALA MET SEQRES 6 A 110 LEU LEU PHE GLU GLN TYR ASN ARG LEU ALA MET PRO ASN SEQRES 7 A 110 MET ARG LEU GLY ASP ALA GLU VAL SER ALA LEU ILE SER SEQRES 8 A 110 TYR LEU GLU GLU GLU THR ALA ARG LEU GLN THR PRO VAL SEQRES 9 A 110 THR ASN ARG GLY ILE PRO HET HEC A 107 75 HETNAM HEC HEME C FORMUL 2 HEC C34 H34 FE N4 O4 HELIX 1 1 SER A 1 CYS A 10 1 10 HELIX 2 2 GLY A 32 GLN A 36 5 5 HELIX 3 3 ASN A 40 LEU A 46 1 7 HELIX 4 4 VAL A 48 GLU A 55 1 8 HELIX 5 5 ASP A 57 ASN A 68 1 12 HELIX 6 6 GLY A 78 GLN A 97 1 20 LINK NE2 HIS A 14 FE HEC A 107 1555 1555 2.00 LINK SD MET A 72 FE HEC A 107 1555 1555 2.65 LINK SG CYS A 10 CAB HEC A 107 1555 1555 1.82 LINK SG CYS A 13 CAC HEC A 107 1555 1555 1.82 SITE 1 AC1 13 PHE A 6 ARG A 9 CYS A 10 CYS A 13 SITE 2 AC1 13 HIS A 14 ILE A 26 LEU A 30 VAL A 33 SITE 3 AC1 13 ARG A 37 TRP A 45 LEU A 63 TYR A 67 SITE 4 AC1 13 MET A 72 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