PDB Short entry for 1K3G HEADER ELECTRON TRANSPORT 03-OCT-01 1K3G TITLE NMR SOLUTION STRUCTURE OF OXIDIZED CYTOCHROME C-553 FROM BACILLUS TITLE 2 PASTEURII CAVEAT 1K3G THERE IS A CHIRALITY ERROR AT THE CA CENTER OF VAL22. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C-553; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 22-92; COMPND 5 SYNONYM: C553; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPOROSARCINA PASTEURII; SOURCE 3 ORGANISM_TAXID: 1474; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PEC86 KEYWDS C-553, HEME, CYTOCHROME, BACILLUS PASTEURII, ELECTRON TRANSFER, KEYWDS 2 ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR L.BANCI,I.BERTINI,S.CIURLI,A.DIKIY,J.DITTMER,A.ROSATO,G.SCIARA, AUTHOR 2 A.R.THOMPSETT REVDAT 5 23-FEB-22 1K3G 1 REMARK LINK REVDAT 4 24-FEB-09 1K3G 1 VERSN REVDAT 3 01-APR-03 1K3G 1 JRNL REVDAT 2 17-APR-02 1K3G 1 JRNL REVDAT 1 31-OCT-01 1K3G 0 JRNL AUTH L.BANCI,I.BERTINI,S.CIURLI,A.DIKIY,J.DITTMER,A.ROSATO, JRNL AUTH 2 G.SCIARA,A.R.THOMPSETT JRNL TITL NMR SOLUTION STRUCTURE, BACKBONE MOBILITY, AND HOMOLOGY JRNL TITL 2 MODELING OF C-TYPE CYTOCHROMES FROM GRAM-POSITIVE BACTERIA. JRNL REF CHEMBIOCHEM V. 3 299 2002 JRNL REFN ISSN 1439-4227 JRNL PMID 11933230 JRNL DOI 10.1002/1439-7633(20020402)3:4<299::AID-CBIC299>3.0.CO;2-0 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.BENINI,A.GONZALEZ,W.R.RYPNIEWSKI,K.S.WILSON, REMARK 1 AUTH 2 J.J.VAN BEEUMEN,S.CIURLI REMARK 1 TITL CRYSTAL STRUCTURE OF OXIDIZED BACILLUS PASTEURII CYTOCHROME REMARK 1 TITL 2 C-553 AT 0.97-A RESOLUTION REMARK 1 REF BIOCHEMISTRY V. 39 13115 2000 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI000402J REMARK 1 REFERENCE 2 REMARK 1 AUTH S.BENINI,M.BORSARI,S.CIURLI,A.DIKIY,M.LAMBORGHINI REMARK 1 TITL MODULATION OF BACILLUS PASTEURII CYTOCHROME C553 REDUCTION REMARK 1 TITL 2 POTENTIAL BY STRUCTURAL AND SOLUTION PARAMETERS REMARK 1 REF J.BIOL.INORG.CHEM. V. 3 371 1998 REMARK 1 REFN ISSN 0949-8257 REMARK 1 DOI 10.1007/S007750050247 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, AMBER 5.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 PSEUDOCONTACT SHIFTS WERE INCLUDED AS CONSTRAINTS BY REMARK 3 MEANS OF MODIFIED DYANA AND SANDER MODULES REMARK 3 (PSEUDODYANA, PSEUDOREM) (BANCI ET AL., 1997) REMARK 4 REMARK 4 1K3G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014512. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 10 MM PHOSPHATE BUFFER REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-3 MM OXIDIZED CYTOCHROME C-553 REMARK 210 IN 10 MM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; HNHA; 1D NOE REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.3.13, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINED ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 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: 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 1 VAL A 22 CB - CA - C ANGL. DEV. = 11.6 DEGREES REMARK 500 1 VAL A 22 CA - CB - CG2 ANGL. DEV. = 9.1 DEGREES REMARK 500 26 VAL A 22 CB - CA - C ANGL. DEV. = 12.1 DEGREES REMARK 500 26 VAL A 22 CA - CB - CG2 ANGL. DEV. = 10.9 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 1 GLN A 29 -8.03 -57.34 REMARK 500 1 LYS A 31 -59.44 -138.97 REMARK 500 1 ALA A 43 -77.93 -131.27 REMARK 500 1 GLN A 68 135.64 177.37 REMARK 500 2 GLN A 30 59.23 -142.60 REMARK 500 2 LYS A 31 -36.39 -173.08 REMARK 500 2 ALA A 43 -71.56 -143.79 REMARK 500 2 GLN A 68 133.56 173.83 REMARK 500 3 GLN A 29 -7.20 -58.12 REMARK 500 3 GLN A 30 33.10 -142.82 REMARK 500 3 LYS A 31 -55.66 -153.92 REMARK 500 3 ALA A 43 -75.83 -137.45 REMARK 500 3 GLN A 68 140.58 176.87 REMARK 500 4 LYS A 31 -38.58 -172.04 REMARK 500 4 SER A 34 -36.75 -38.92 REMARK 500 4 ALA A 43 -76.90 -143.52 REMARK 500 4 LYS A 50 40.87 -109.31 REMARK 500 4 GLN A 68 131.38 176.31 REMARK 500 4 GLU A 90 35.65 -84.70 REMARK 500 5 GLN A 30 48.60 -146.43 REMARK 500 5 LYS A 31 -39.70 -162.46 REMARK 500 5 SER A 34 -39.19 -37.38 REMARK 500 5 ALA A 43 -79.77 -143.60 REMARK 500 5 GLN A 68 130.18 173.98 REMARK 500 6 GLN A 30 44.57 -142.56 REMARK 500 6 LYS A 31 -39.98 -157.36 REMARK 500 6 ALA A 43 -73.10 -151.79 REMARK 500 6 GLN A 68 136.28 176.51 REMARK 500 7 LYS A 31 -58.61 -161.28 REMARK 500 7 ALA A 43 -80.34 -152.52 REMARK 500 7 GLN A 68 139.13 170.46 REMARK 500 8 LYS A 31 -38.97 -167.96 REMARK 500 8 SER A 34 -38.55 -37.92 REMARK 500 8 ALA A 43 -78.10 -135.39 REMARK 500 8 GLN A 68 132.87 174.30 REMARK 500 9 GLN A 30 43.67 -141.71 REMARK 500 9 LYS A 31 -39.73 -153.18 REMARK 500 9 SER A 34 -37.01 -37.75 REMARK 500 9 ALA A 43 -72.98 -155.08 REMARK 500 9 GLN A 68 139.63 167.08 REMARK 500 10 LYS A 31 -38.90 -166.43 REMARK 500 10 SER A 34 -39.31 -36.92 REMARK 500 10 ALA A 43 -76.77 -156.24 REMARK 500 10 GLN A 68 140.72 167.03 REMARK 500 11 GLN A 30 55.10 -144.67 REMARK 500 11 LYS A 31 -38.29 -167.25 REMARK 500 11 ALA A 43 -79.55 -135.95 REMARK 500 11 GLN A 68 138.38 166.73 REMARK 500 12 ALA A 24 -64.12 -105.18 REMARK 500 12 LYS A 31 -56.67 -152.37 REMARK 500 REMARK 500 THIS ENTRY HAS 125 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 VAL A 22 ASP A 23 11 133.18 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 5 TYR A 55 0.08 SIDE CHAIN REMARK 500 9 TYR A 55 0.07 SIDE CHAIN REMARK 500 23 TYR A 55 0.09 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 93 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 36 NE2 REMARK 620 2 HEC A 93 NA 98.0 REMARK 620 3 HEC A 93 NB 89.5 90.6 REMARK 620 4 HEC A 93 NC 86.1 173.8 94.0 REMARK 620 5 HEC A 93 ND 91.1 87.5 178.0 87.9 REMARK 620 6 MET A 71 SD 173.2 82.1 97.3 93.2 82.2 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 93 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C75 RELATED DB: PDB REMARK 900 1C75 IS THE X-RAY STRUCTURE OF THE CYTOCHROME C553 FROM B. REMARK 900 PASTEURII. REMARK 900 RELATED ID: 1K3H RELATED DB: PDB REMARK 900 1K3H IS THE MINIMIZED AVERAGE OF OXIDIZED CYTOCHROME C-553 FROM B. REMARK 900 PASTEURII. DBREF 1K3G A 22 92 UNP P82599 CY553_BACPA 22 92 SEQRES 1 A 71 VAL ASP ALA GLU ALA VAL VAL GLN GLN LYS CYS ILE SER SEQRES 2 A 71 CYS HIS GLY GLY ASP LEU THR GLY ALA SER ALA PRO ALA SEQRES 3 A 71 ILE ASP LYS ALA GLY ALA ASN TYR SER GLU GLU GLU ILE SEQRES 4 A 71 LEU ASP ILE ILE LEU ASN GLY GLN GLY GLY MET PRO GLY SEQRES 5 A 71 GLY ILE ALA LYS GLY ALA GLU ALA GLU ALA VAL ALA ALA SEQRES 6 A 71 TRP LEU ALA GLU LYS LYS HET HEC A 93 75 HETNAM HEC HEME C FORMUL 2 HEC C34 H34 FE N4 O4 HELIX 1 1 ASP A 23 GLN A 29 1 7 HELIX 2 2 CYS A 32 GLY A 37 1 6 HELIX 3 3 LYS A 50 TYR A 55 1 6 HELIX 4 4 SER A 56 GLY A 67 1 12 HELIX 5 5 GLY A 78 LYS A 91 1 14 LINK SG CYS A 32 CAB HEC A 93 1555 1555 1.81 LINK SG CYS A 35 CAC HEC A 93 1555 1555 1.81 LINK NE2 HIS A 36 FE HEC A 93 1555 1555 1.98 LINK SD MET A 71 FE HEC A 93 1555 1555 2.41 SITE 1 AC1 17 LYS A 31 CYS A 32 CYS A 35 HIS A 36 SITE 2 AC1 17 ALA A 45 PRO A 46 ILE A 48 TYR A 55 SITE 3 AC1 17 ILE A 60 ILE A 63 ILE A 64 GLN A 68 SITE 4 AC1 17 GLY A 69 GLY A 70 MET A 71 ILE A 75 SITE 5 AC1 17 VAL A 84 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