PDB Short entry for 1SR3 HEADER CHAPERONE 22-MAR-04 1SR3 TITLE SOLUTION STRUCTURE OF THE HEME CHAPERONE CCME OF ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: APO-CCME; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SOLUBLE APO-CCME-H6(C-TERMINAL DOMAIN); COMPND 5 SYNONYM: CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCME; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 CELLULAR_LOCATION: PERIPLASM; SOURCE 5 GENE: CCME; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: EC06; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PEC415 KEYWDS OB FOLD, BETA BARREL, FLEXIBLE C-TERMINAL DOMAIN, CHAPERONE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.ENGGIST,L.THONY-MEYER,P.GUNTERT,K.PERVUSHIN REVDAT 3 02-MAR-22 1SR3 1 REMARK SEQADV REVDAT 2 24-FEB-09 1SR3 1 VERSN REVDAT 1 06-APR-04 1SR3 0 SPRSDE 06-APR-04 1SR3 1LIZ JRNL AUTH E.ENGGIST,L.THONY-MEYER,P.GUNTERT,K.PERVUSHIN JRNL TITL NMR STRUCTURE OF THE HEME CHAPERONE CCME REVEALS A NOVEL JRNL TITL 2 FUNCTIONAL MOTIF JRNL REF STRUCTURE V. 10 1551 2002 JRNL REFN ISSN 0969-2126 JRNL PMID 12429096 JRNL DOI 10.1016/S0969-2126(02)00885-7 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA REMARK 3 AUTHORS : GUNTERT, P. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1SR3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000021939. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.1MM APO-CCME-H6 U-98% 13C; U REMARK 210 -98% 15N; 50MM PHOSPHATE BUFFER, REMARK 210 PH 7.2, 300MM NACL, 90% H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_13C- REMARK 210 SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY; 2D_TROSY; 3D_ REMARK 210 TROSY_HNCA; 3D_TROSY_HNCACB; REMARK 210 CBCA(CO)NH; HCCH-TOCSA; 15N_ REMARK 210 EDITED_TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY, PROSA, CANDID REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED 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 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 GLU A 144 REMARK 465 ALA A 145 REMARK 465 ASN A 146 REMARK 465 HIS A 147 REMARK 465 ARG A 148 REMARK 465 ARG A 149 REMARK 465 PRO A 150 REMARK 465 ALA A 151 REMARK 465 SER A 152 REMARK 465 VAL A 153 REMARK 465 TYR A 154 REMARK 465 LYS A 155 REMARK 465 ASP A 156 REMARK 465 PRO A 157 REMARK 465 ALA A 158 REMARK 465 SER A 159 REMARK 465 HIS A 160 REMARK 465 HIS A 161 REMARK 465 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 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 62 CA - CB - CG1 ANGL. DEV. = 16.7 DEGREES REMARK 500 4 ARG A 61 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 7 VAL A 62 CA - CB - CG1 ANGL. DEV. = 17.6 DEGREES REMARK 500 9 VAL A 62 CA - CB - CG1 ANGL. DEV. = 12.7 DEGREES REMARK 500 9 VAL A 110 CA - CB - CG1 ANGL. DEV. = 9.2 DEGREES REMARK 500 11 LEU A 44 CB - CG - CD1 ANGL. DEV. = 12.8 DEGREES REMARK 500 14 VAL A 111 CA - CB - CG2 ANGL. DEV. = 10.2 DEGREES REMARK 500 15 LEU A 44 CB - CG - CD1 ANGL. DEV. = 10.8 DEGREES REMARK 500 16 LEU A 44 CB - CG - CD2 ANGL. DEV. = 10.7 DEGREES REMARK 500 19 VAL A 109 CA - CB - CG1 ANGL. DEV. = 11.9 DEGREES REMARK 500 20 VAL A 66 CA - CB - CG1 ANGL. DEV. = 11.7 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 SER A 32 161.67 139.97 REMARK 500 1 ASN A 33 177.66 61.81 REMARK 500 1 ASP A 35 -161.73 52.36 REMARK 500 1 ARG A 48 -19.74 -19.05 REMARK 500 1 GLU A 49 -75.09 -121.36 REMARK 500 1 THR A 50 31.07 -164.94 REMARK 500 1 GLN A 52 175.97 176.23 REMARK 500 1 VAL A 71 94.31 -61.73 REMARK 500 1 ALA A 87 6.65 -61.34 REMARK 500 1 LYS A 117 -72.34 -150.84 REMARK 500 1 GLU A 125 -45.72 -146.05 REMARK 500 1 VAL A 126 133.70 58.97 REMARK 500 1 HIS A 130 41.61 -71.64 REMARK 500 1 ASP A 131 -65.82 67.69 REMARK 500 1 GLU A 132 154.19 65.47 REMARK 500 1 ASN A 133 -50.17 -147.10 REMARK 500 1 TYR A 134 109.26 66.63 REMARK 500 1 VAL A 139 -53.33 -165.20 REMARK 500 1 LYS A 141 20.79 -148.89 REMARK 500 2 ASN A 33 -56.47 -145.54 REMARK 500 2 ASP A 35 151.66 -37.23 REMARK 500 2 ARG A 48 -16.00 -42.70 REMARK 500 2 GLU A 49 -63.02 -122.67 REMARK 500 2 THR A 50 21.56 -170.07 REMARK 500 2 GLN A 52 168.63 173.82 REMARK 500 2 VAL A 71 105.78 -59.68 REMARK 500 2 ARG A 73 129.25 42.67 REMARK 500 2 GLU A 88 -80.84 -112.84 REMARK 500 2 LEU A 99 151.87 67.13 REMARK 500 2 GLU A 116 -64.09 -103.44 REMARK 500 2 LYS A 117 158.41 167.05 REMARK 500 2 GLU A 125 -41.48 -139.61 REMARK 500 2 VAL A 126 127.71 59.28 REMARK 500 2 HIS A 130 -91.90 -76.78 REMARK 500 2 ASP A 131 45.39 -162.81 REMARK 500 3 ARG A 31 -42.73 -149.98 REMARK 500 3 SER A 32 -65.41 65.75 REMARK 500 3 ASN A 33 135.31 61.72 REMARK 500 3 ILE A 34 165.72 61.11 REMARK 500 3 ARG A 48 -77.27 -18.18 REMARK 500 3 GLU A 49 -87.27 -66.40 REMARK 500 3 THR A 50 36.92 -174.38 REMARK 500 3 GLN A 52 -173.31 -174.42 REMARK 500 3 VAL A 71 104.45 -57.89 REMARK 500 3 ARG A 73 165.34 54.20 REMARK 500 3 GLU A 88 -71.33 -103.12 REMARK 500 3 LEU A 99 149.84 89.43 REMARK 500 3 GLU A 116 -72.34 -93.39 REMARK 500 3 LYS A 117 -86.07 -141.86 REMARK 500 3 GLU A 125 -38.31 -144.41 REMARK 500 REMARK 500 THIS ENTRY HAS 371 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 LYS A 47 ARG A 48 1 -135.21 REMARK 500 ALA A 142 MET A 143 1 147.88 REMARK 500 VAL A 62 GLY A 63 2 148.84 REMARK 500 LYS A 47 ARG A 48 4 -143.80 REMARK 500 LYS A 47 ARG A 48 7 -142.91 REMARK 500 LYS A 47 ARG A 48 8 -136.63 REMARK 500 GLY A 106 GLN A 107 9 145.20 REMARK 500 ARG A 48 GLU A 49 10 146.41 REMARK 500 ARG A 48 GLU A 49 11 148.90 REMARK 500 ALA A 142 MET A 143 13 145.34 REMARK 500 SER A 32 ASN A 33 16 142.45 REMARK 500 ALA A 142 MET A 143 17 148.78 REMARK 500 ASP A 35 LEU A 36 18 148.20 REMARK 500 LYS A 47 ARG A 48 18 -142.46 REMARK 500 THR A 50 GLN A 51 19 -147.51 REMARK 500 LYS A 47 ARG A 48 20 -138.51 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 61 0.08 SIDE CHAIN REMARK 500 2 ARG A 48 0.08 SIDE CHAIN REMARK 500 3 ARG A 59 0.08 SIDE CHAIN REMARK 500 3 ARG A 104 0.08 SIDE CHAIN REMARK 500 6 ARG A 61 0.08 SIDE CHAIN REMARK 500 7 ARG A 31 0.08 SIDE CHAIN REMARK 500 7 TYR A 38 0.08 SIDE CHAIN REMARK 500 7 ARG A 59 0.10 SIDE CHAIN REMARK 500 7 ARG A 73 0.16 SIDE CHAIN REMARK 500 7 ARG A 104 0.08 SIDE CHAIN REMARK 500 8 TYR A 85 0.06 SIDE CHAIN REMARK 500 8 ARG A 104 0.10 SIDE CHAIN REMARK 500 9 TYR A 38 0.09 SIDE CHAIN REMARK 500 9 ARG A 104 0.07 SIDE CHAIN REMARK 500 10 ARG A 31 0.09 SIDE CHAIN REMARK 500 11 ARG A 73 0.10 SIDE CHAIN REMARK 500 14 TYR A 95 0.08 SIDE CHAIN REMARK 500 15 ARG A 59 0.09 SIDE CHAIN REMARK 500 15 ARG A 104 0.10 SIDE CHAIN REMARK 500 16 TYR A 85 0.08 SIDE CHAIN REMARK 500 17 TYR A 38 0.07 SIDE CHAIN REMARK 500 17 ARG A 61 0.11 SIDE CHAIN REMARK 500 18 ARG A 48 0.08 SIDE CHAIN REMARK 500 18 ARG A 61 0.08 SIDE CHAIN REMARK 500 18 TYR A 85 0.07 SIDE CHAIN REMARK 500 19 ARG A 31 0.11 SIDE CHAIN REMARK 500 19 TYR A 45 0.07 SIDE CHAIN REMARK 500 19 TYR A 134 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5526 RELATED DB: BMRB REMARK 900 5526 IS CHEMICAL SHIFT OF THE SAME PROTEIN DBREF 1SR3 A 30 159 UNP P69490 CCME_ECOLI 30 159 SEQADV 1SR3 HIS A 160 UNP P69490 INSERTION SEQADV 1SR3 HIS A 161 UNP P69490 INSERTION SEQADV 1SR3 HIS A 162 UNP P69490 INSERTION SEQADV 1SR3 HIS A 163 UNP P69490 INSERTION SEQADV 1SR3 HIS A 164 UNP P69490 INSERTION SEQADV 1SR3 HIS A 165 UNP P69490 INSERTION SEQRES 1 A 136 LEU ARG SER ASN ILE ASP LEU PHE TYR THR PRO GLY GLU SEQRES 2 A 136 ILE LEU TYR GLY LYS ARG GLU THR GLN GLN MET PRO GLU SEQRES 3 A 136 VAL GLY GLN ARG LEU ARG VAL GLY GLY MET VAL MET PRO SEQRES 4 A 136 GLY SER VAL GLN ARG ASP PRO ASN SER LEU LYS VAL THR SEQRES 5 A 136 PHE THR ILE TYR ASP ALA GLU GLY SER VAL ASP VAL SER SEQRES 6 A 136 TYR GLU GLY ILE LEU PRO ASP LEU PHE ARG GLU GLY GLN SEQRES 7 A 136 GLY VAL VAL VAL GLN GLY GLU LEU GLU LYS GLY ASN HIS SEQRES 8 A 136 ILE LEU ALA LYS GLU VAL LEU ALA LYS HIS ASP GLU ASN SEQRES 9 A 136 TYR THR PRO PRO GLU VAL GLU LYS ALA MET GLU ALA ASN SEQRES 10 A 136 HIS ARG ARG PRO ALA SER VAL TYR LYS ASP PRO ALA SER SEQRES 11 A 136 HIS HIS HIS HIS HIS HIS HELIX 1 1 PRO A 136 LYS A 141 1 6 SHEET 1 A 7 GLN A 72 ARG A 73 0 SHEET 2 A 7 LYS A 79 TYR A 85 -1 O THR A 81 N GLN A 72 SHEET 3 A 7 SER A 90 GLU A 96 -1 O TYR A 95 N VAL A 80 SHEET 4 A 7 HIS A 120 ALA A 123 1 O ALA A 123 N SER A 94 SHEET 5 A 7 GLY A 108 LEU A 115 -1 N GLU A 114 O LEU A 122 SHEET 6 A 7 ARG A 59 VAL A 66 -1 N LEU A 60 O GLY A 113 SHEET 7 A 7 LYS A 79 TYR A 85 -1 O TYR A 85 N MET A 65 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