HEADER CHAPERONE 30-APR-02 1LM0 TITLE SOLUTION STRUCTURE AND CHARACTERIZATION OF THE HEME CHAPERONE CCME COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C MATURATION PROTEIN E; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WATER SOLUBLE DOMAIN OF CCME; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHEWANELLA PUTREFACIENS; SOURCE 3 ORGANISM_TAXID: 24; SOURCE 4 GENE: CCME; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPB10 KEYWDS ALL-BETA PROTEIN, HEME DELIVERY, CYTOCHROME C MATURATION, OB- KEYWDS 2 (OLIGONUCLEOTIDE BINDING)FOLD, CHAPERONE EXPDTA SOLUTION NMR NUMMDL 35 AUTHOR F.ARNESANO,L.BANCI,P.D.BARKER,I.BERTINI,A.ROSATO,X.C.SU,M.S.VIEZZOLI REVDAT 5 22-MAY-24 1LM0 1 REMARK REVDAT 4 23-FEB-22 1LM0 1 REMARK SEQADV REVDAT 3 24-FEB-09 1LM0 1 VERSN REVDAT 2 18-FEB-03 1LM0 3 ATOM REVDAT 1 25-DEC-02 1LM0 0 JRNL AUTH F.ARNESANO,L.BANCI,P.D.BARKER,I.BERTINI,A.ROSATO,X.C.SU, JRNL AUTH 2 M.S.VIEZZOLI JRNL TITL SOLUTION STRUCTURE AND CHARACTERIZATION OF THE HEME JRNL TITL 2 CHAPERONE CCME JRNL REF BIOCHEMISTRY V. 41 13587 2002 JRNL REFN ISSN 0006-2960 JRNL PMID 12427019 JRNL DOI 10.1021/BI026362W 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), PEARLMAN, CASE, CALDWELL, ROSS, REMARK 3 CHEATHAM, FERGUSON, SEIBEL, SINGH, WEINER, KOLLMAN REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1866 MEANINGFUL NOES AND 89 DIHEDRAL REMARK 3 ANGLE CONSTRAINTS REMARK 4 REMARK 4 1LM0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1000016071. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 20 MM PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.0 MM APOCCME, 20 MM PHOSPHATE, REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_13C REMARK 210 -SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_NOESY; HNHA; HNCO; REMARK 210 HNHB; CBCANH; CC(CO)NH; CBCA(CO) REMARK 210 NH REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.3, DYANA 1.5, CORMA REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYANAMICS, RESTRAINED REMARK 210 ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 35 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED CONFORMER MODELS REMARK 210 ARE THE 35 STRUCTURES WITH THE REMARK 210 LOWEST TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON 13C AND 15N DOUBLE LABELED APOCCME. 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 1-35 REMARK 465 RES C SSSEQI REMARK 465 PHE A 26 REMARK 465 ALA A 27 REMARK 465 ALA A 28 REMARK 465 ASP A 29 REMARK 465 LEU A 30 REMARK 465 ASN A 31 REMARK 465 GLU A 133 REMARK 465 ASN A 134 REMARK 465 TYR A 135 REMARK 465 MET A 136 REMARK 465 PRO A 137 REMARK 465 PRO A 138 REMARK 465 GLU A 139 REMARK 465 VAL A 140 REMARK 465 ALA A 141 REMARK 465 GLU A 142 REMARK 465 ALA A 143 REMARK 465 MET A 144 REMARK 465 GLY A 145 REMARK 465 GLN A 146 REMARK 465 LYS A 147 REMARK 465 HIS A 148 REMARK 465 GLU A 149 REMARK 465 LYS A 150 REMARK 465 LEU A 151 REMARK 465 ASP A 152 REMARK 465 TYR A 153 REMARK 465 SER A 154 REMARK 465 GLN A 155 REMARK 465 GLN A 156 REMARK 465 LYS A 157 REMARK 465 SER A 158 REMARK 465 ALA A 159 REMARK 465 THR A 160 REMARK 465 GLN A 161 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 2 TYR A 96 CB - CG - CD2 ANGL. DEV. = -4.0 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 ILE A 43 33.00 -71.76 REMARK 500 1 VAL A 44 -76.41 -111.99 REMARK 500 1 LYS A 47 -105.30 -139.79 REMARK 500 1 LYS A 53 -68.72 -101.73 REMARK 500 1 LEU A 103 6.79 59.99 REMARK 500 1 PHE A 104 88.67 59.24 REMARK 500 1 ASP A 119 70.01 12.16 REMARK 500 2 LYS A 47 -155.39 -156.49 REMARK 500 2 LYS A 53 -71.94 -121.41 REMARK 500 2 SER A 70 1.92 -150.41 REMARK 500 2 PRO A 101 -95.34 -69.21 REMARK 500 2 ASP A 102 44.95 -76.15 REMARK 500 2 LEU A 103 -11.12 60.82 REMARK 500 2 PHE A 104 88.36 64.57 REMARK 500 2 ASP A 119 -71.18 -163.12 REMARK 500 2 THR A 125 -44.42 -140.12 REMARK 500 3 ASN A 35 89.06 -151.58 REMARK 500 3 PRO A 40 -72.96 -6.37 REMARK 500 3 LYS A 47 -124.15 -150.18 REMARK 500 3 LYS A 53 -78.93 -124.36 REMARK 500 3 SER A 87 26.96 47.84 REMARK 500 3 LEU A 88 -67.66 -101.60 REMARK 500 3 LEU A 103 22.01 44.89 REMARK 500 3 PHE A 104 110.94 51.00 REMARK 500 3 ASP A 119 45.06 27.25 REMARK 500 3 THR A 125 -41.76 -136.05 REMARK 500 3 LYS A 130 47.69 -79.02 REMARK 500 3 HIS A 131 52.62 -146.59 REMARK 500 4 LYS A 47 -89.07 -30.93 REMARK 500 4 VAL A 68 71.98 -116.98 REMARK 500 4 PRO A 75 28.90 -75.45 REMARK 500 4 LEU A 88 32.25 -91.86 REMARK 500 4 GLU A 91 96.15 -66.79 REMARK 500 4 ASP A 97 -82.43 -85.94 REMARK 500 4 PRO A 101 -85.11 -67.90 REMARK 500 4 LEU A 103 41.75 34.63 REMARK 500 4 PHE A 104 74.56 31.48 REMARK 500 4 ASP A 119 72.56 -6.17 REMARK 500 5 LEU A 34 -52.72 -144.38 REMARK 500 5 LYS A 47 -153.87 -152.40 REMARK 500 5 THR A 48 -58.16 -28.97 REMARK 500 5 LYS A 53 -63.03 -105.81 REMARK 500 5 THR A 67 -85.43 -49.27 REMARK 500 5 VAL A 68 -40.93 174.45 REMARK 500 5 ASP A 102 47.70 39.74 REMARK 500 5 LEU A 103 13.52 48.76 REMARK 500 5 PHE A 104 114.29 51.49 REMARK 500 5 LYS A 130 58.14 -153.56 REMARK 500 6 ILE A 43 36.05 -74.17 REMARK 500 6 VAL A 44 -68.68 -123.38 REMARK 500 REMARK 500 THIS ENTRY HAS 440 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 GLY A 57 GLN A 58 2 -81.36 REMARK 500 PHE A 104 ARG A 105 4 -124.97 REMARK 500 LEU A 103 PHE A 104 5 -148.96 REMARK 500 ARG A 105 GLU A 106 5 -148.26 REMARK 500 SER A 87 LEU A 88 9 -150.00 REMARK 500 ARG A 105 GLU A 106 9 146.31 REMARK 500 PHE A 104 ARG A 105 10 -119.07 REMARK 500 ARG A 105 GLU A 106 11 140.29 REMARK 500 LEU A 34 ASN A 35 19 -129.95 REMARK 500 SER A 87 LEU A 88 19 -145.74 REMARK 500 LEU A 103 PHE A 104 22 -148.06 REMARK 500 ARG A 105 GLU A 106 22 -126.67 REMARK 500 SER A 87 LEU A 88 26 -147.75 REMARK 500 ARG A 105 GLU A 106 26 149.88 REMARK 500 SER A 87 LEU A 88 27 -148.98 REMARK 500 PHE A 104 ARG A 105 27 -137.59 REMARK 500 ARG A 105 GLU A 106 27 -147.31 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 73 0.08 SIDE CHAIN REMARK 500 1 PHE A 104 0.09 SIDE CHAIN REMARK 500 2 TYR A 38 0.08 SIDE CHAIN REMARK 500 2 TYR A 96 0.15 SIDE CHAIN REMARK 500 2 PHE A 104 0.09 SIDE CHAIN REMARK 500 3 TYR A 38 0.07 SIDE CHAIN REMARK 500 4 PHE A 104 0.09 SIDE CHAIN REMARK 500 5 TYR A 96 0.07 SIDE CHAIN REMARK 500 6 ARG A 105 0.12 SIDE CHAIN REMARK 500 7 TYR A 38 0.08 SIDE CHAIN REMARK 500 7 PHE A 104 0.11 SIDE CHAIN REMARK 500 8 TYR A 38 0.09 SIDE CHAIN REMARK 500 8 PHE A 104 0.10 SIDE CHAIN REMARK 500 9 ARG A 61 0.08 SIDE CHAIN REMARK 500 10 PHE A 104 0.09 SIDE CHAIN REMARK 500 11 ARG A 59 0.08 SIDE CHAIN REMARK 500 12 TYR A 96 0.15 SIDE CHAIN REMARK 500 12 ARG A 105 0.13 SIDE CHAIN REMARK 500 13 TYR A 38 0.07 SIDE CHAIN REMARK 500 13 TYR A 96 0.08 SIDE CHAIN REMARK 500 13 PHE A 104 0.09 SIDE CHAIN REMARK 500 14 TYR A 96 0.09 SIDE CHAIN REMARK 500 15 TYR A 96 0.16 SIDE CHAIN REMARK 500 16 ARG A 59 0.11 SIDE CHAIN REMARK 500 16 ARG A 105 0.10 SIDE CHAIN REMARK 500 17 TYR A 96 0.07 SIDE CHAIN REMARK 500 19 ARG A 59 0.08 SIDE CHAIN REMARK 500 19 TYR A 96 0.08 SIDE CHAIN REMARK 500 19 ARG A 105 0.13 SIDE CHAIN REMARK 500 20 PHE A 104 0.13 SIDE CHAIN REMARK 500 22 TYR A 96 0.07 SIDE CHAIN REMARK 500 23 TYR A 38 0.07 SIDE CHAIN REMARK 500 23 ARG A 59 0.09 SIDE CHAIN REMARK 500 23 PHE A 82 0.08 SIDE CHAIN REMARK 500 23 TYR A 96 0.09 SIDE CHAIN REMARK 500 24 TYR A 38 0.18 SIDE CHAIN REMARK 500 26 PHE A 104 0.09 SIDE CHAIN REMARK 500 27 TYR A 38 0.22 SIDE CHAIN REMARK 500 27 PHE A 104 0.08 SIDE CHAIN REMARK 500 28 PHE A 82 0.09 SIDE CHAIN REMARK 500 28 PHE A 104 0.11 SIDE CHAIN REMARK 500 28 ARG A 105 0.10 SIDE CHAIN REMARK 500 29 TYR A 96 0.14 SIDE CHAIN REMARK 500 30 TYR A 96 0.08 SIDE CHAIN REMARK 500 31 TYR A 96 0.15 SIDE CHAIN REMARK 500 32 TYR A 38 0.13 SIDE CHAIN REMARK 500 32 TYR A 96 0.15 SIDE CHAIN REMARK 500 32 PHE A 104 0.17 SIDE CHAIN REMARK 500 33 TYR A 96 0.09 SIDE CHAIN REMARK 500 33 PHE A 104 0.12 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 52 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J6Q RELATED DB: PDB REMARK 900 PDB-ID 1J6Q REPRESENTS THE MEAN OF ENERGY MINIMIZED STRUCTURES. DBREF 1LM0 A 30 161 UNP O52690 O52690_SHEPU 30 161 SEQADV 1LM0 PHE A 26 UNP O52690 CLONING ARTIFACT SEQADV 1LM0 ALA A 27 UNP O52690 CLONING ARTIFACT SEQADV 1LM0 ALA A 28 UNP O52690 CLONING ARTIFACT SEQADV 1LM0 ASP A 29 UNP O52690 CLONING ARTIFACT SEQRES 1 A 136 PHE ALA ALA ASP LEU ASN SER ASN LEU ASN LEU PHE TYR SEQRES 2 A 136 THR PRO SER GLU ILE VAL ASN GLY LYS THR ASP THR GLY SEQRES 3 A 136 VAL LYS PRO GLU ALA GLY GLN ARG ILE ARG VAL GLY GLY SEQRES 4 A 136 MET VAL THR VAL GLY SER MET VAL ARG ASP PRO ASN SER SEQRES 5 A 136 LEU HIS VAL GLN PHE ALA VAL HIS ASP SER LEU GLY GLY SEQRES 6 A 136 GLU ILE LEU VAL THR TYR ASP ASP LEU LEU PRO ASP LEU SEQRES 7 A 136 PHE ARG GLU GLY GLN GLY ILE VAL ALA GLN GLY VAL LEU SEQRES 8 A 136 GLY GLU ASP GLY LYS LEU ALA ALA THR GLU VAL LEU ALA SEQRES 9 A 136 LYS HIS ASP GLU ASN TYR MET PRO PRO GLU VAL ALA GLU SEQRES 10 A 136 ALA MET GLY GLN LYS HIS GLU LYS LEU ASP TYR SER GLN SEQRES 11 A 136 GLN LYS SER ALA THR GLN HELIX 1 1 LEU A 100 PHE A 104 5 5 SHEET 1 A 7 PHE A 37 TYR A 38 0 SHEET 2 A 7 ARG A 59 MET A 65 1 O ARG A 61 N TYR A 38 SHEET 3 A 7 GLY A 109 GLU A 118 -1 O ALA A 112 N VAL A 62 SHEET 4 A 7 LYS A 121 LEU A 128 -1 O LEU A 128 N VAL A 111 SHEET 5 A 7 ILE A 92 THR A 95 1 N THR A 95 O ALA A 124 SHEET 6 A 7 GLN A 81 VAL A 84 -1 N PHE A 82 O VAL A 94 SHEET 7 A 7 MET A 71 VAL A 72 -1 N VAL A 72 O GLN A 81 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