HEADER CHAPERONE 29-DEC-08 2KCT TITLE SOLUTION NMR STRUCTURE OF THE OB-FOLD DOMAIN OF HEME CHAPERONE CCME TITLE 2 FROM DESULFOVIBRIO VULGARIS. NORTHEAST STRUCTURAL GENOMICS TARGET TITLE 3 DVR115G. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCME; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS STR. HILDENBOROUGH; SOURCE 3 ORGANISM_TAXID: 882; SOURCE 4 GENE: CCME, DVU_1051; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: DVR115G-21.2 KEYWDS SOLUTION NMR STRUCTURE, HEME CHAPERONE, CYTOCHROME C BIOGENESIS, OB- KEYWDS 2 FOLD DOMAIN, NESG, PSI-2, STRUCTURAL GENOMICS, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, BIOSYNTHETIC KEYWDS 4 PROTEIN, CHAPERONE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,P.ROSSI,H.LEE,A.LEMAK,H.WANG,E.L.FOOTE,M.JIANG,R.XIAO, AUTHOR 2 R.NAIR,G.V.T.SWAPNA,T.B.ACTON,B.ROST,J.K.EVERETT,G.T.MONTELIONE, AUTHOR 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 3 01-MAY-24 2KCT 1 REMARK REVDAT 2 06-NOV-19 2KCT 1 REMARK REVDAT 1 10-FEB-09 2KCT 0 JRNL AUTH J.M.ARAMINI,P.ROSSI,H.LEE,A.LEMAK,H.WANG,E.L.FOOTE,M.JIANG, JRNL AUTH 2 R.XIAO,R.NAIR,G.V.T.SWAPNA,T.B.ACTON,B.ROST,J.K.EVERETT, JRNL AUTH 3 G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE OB-FOLD DOMAIN OF HEME JRNL TITL 2 CHAPERONE CCME FROM DESULFOVIBRIO VULGARIS. NORTHEAST JRNL TITL 3 STRUCTURAL GENOMICS TARGET DVR115G. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 1384 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS AND 79 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND REMARK 3 CONSTRAINTS (16.8 CONSTRAINTS PER RESIDUE, 6.0 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 43 TO 130 BY PSVS REMARK 3 1.3). IN ADDITION, 49 RESOLVED N-H RESIDUAL DIPOLAR COUPLINGS REMARK 3 FOR ORDERED RESIDUES WERE INCLUDED IN ALL STRUCTURE REMARK 3 CALCULATIONS. STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY REMARK 3 USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST REMARK 3 TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR REMARK 3 DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH REMARK 3 PARAM19. REMARK 4 REMARK 4 2KCT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000100960. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.3 MM [U-100% 13C; U-100% 15N] REMARK 210 DVR115G, 20 MM AMMONIUM ACETATE, REMARK 210 200 MM SODIUM CHLORIDE, 5 MM REMARK 210 CALCIUM CHLORIDE, 10 MM DTT, REMARK 210 0.02 % SODIUM AZIDE, 50 UM DSS, REMARK 210 90% H2O/10% D2O; 0.56 MM [U-5% REMARK 210 13C; U-100% 15N] DVR115G, 20 MM REMARK 210 AMMONIUM ACETATE, 200 MM SODIUM REMARK 210 CHLORIDE, 5 MM CALCIUM CHLORIDE, REMARK 210 10 MM DTT, 0.02 % SODIUM AZIDE, REMARK 210 50 UM DSS, 90% H2O/10% D2O; 10 % REMARK 210 [U-5% 13C; U-100% 15N] DVR115G, REMARK 210 4.2 % PEG/HEXANOL, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D SIMULTANEOUS CN NOESY; 3D 1H- REMARK 210 13C NOESY AROMATIC; 2D 1H-13C REMARK 210 HSQC HIGH RES. (L/V METHYL REMARK 210 STEREOASSIGNMENT); 3D HNCO; 3D REMARK 210 HN(CO)CA; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D HN(CA) REMARK 210 CO; 3D C(CO)NH TOCSY; 3D HCCH- REMARK 210 COSY ALIPHATIC; 3D HCCH- TOCSY REMARK 210 ALIPHATIC; 3D (H)CCH- TOCSY REMARK 210 ALIPHATIC; 3D HNHA; 2D 1H-15N REMARK 210 HETNOE; 1D 1H-15N T1 AND T2; 2D REMARK 210 1H-15N TROSY (FOR N-H RDC'S) REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, VNMRJ 2.1B, NMRPIPE REMARK 210 2.3, SPARKY 3.112, PINE, REMARK 210 AUTOASSIGN 2.4.0, CYANA 3.0, REMARK 210 AUTOSTRUCTURE 2.2.1, PSVS 1.3, REMARK 210 PDBSTAT 5.1, PALES REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE PROTEIN IS MONOMERIC BY GEL FILTRATION REMARK 210 CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 REMARK 210 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE REMARK 210 RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS REMARK 210 WERE MADE USING AUTOASSIGN AND PINE, AND THE SIDE CHAIN REMARK 210 ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY REMARK 210 ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/ REMARK 210 PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. REMARK 210 ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE CONSTRAINED REMARK 210 IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED ON REMARK 210 PROCHECK. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C- REMARK 210 TERMINAL HHHHHH): BACKBONE, 98.6%, SIDE CHAIN, 97.2%, REMARK 210 AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC REMARK 210 SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR REMARK 210 RESIDUES 43 TO 130, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) REMARK 210 + S(PSI) > 1.8] COMPRISE: 52-67,70-79,86-112,115-127: (A) RMSD REMARK 210 (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 0.9. (B) RAMACHANDRAN REMARK 210 STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 93.9%, REMARK 210 ADDITIONALLY ALLOWED, 6.1%, GENEROUSLY ALLOWED, 0.0%, REMARK 210 DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES REMARK 210 (RAW/Z-): PHI-PSI, -0.62/-2.12, ALL, -0.43/-2.54. (D) REMARK 210 MOLPROBITY CLASH SCORE (RAW/Z-): 10.87/-0.34 (E) RPF SCORES REMARK 210 FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 43-130): RECALL, REMARK 210 0.984, PRECISION, 0.915, F-MEASURE, 0.948, DP-SCORE, 0.795. REMARK 210 (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 4. (G) AGREEMENT REMARK 210 WITH RESIDUAL DIPOLAR COUPLINGS (20 MODELS): CORRELATION REMARK 210 COEFFICIENT (R): 0.995 (0.001); Q RMS: 0.096 (0.011). THE C- REMARK 210 TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT REMARK 210 INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED REMARK 210 FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES REMARK 210 ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 43-51,68-69, REMARK 210 80-85,113-114,128-130. 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 HIS A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 HIS A 135 REMARK 465 HIS A 136 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 HIS A 51 95.04 -64.24 REMARK 500 1 ASP A 68 98.07 -64.97 REMARK 500 1 PRO A 113 104.43 -57.70 REMARK 500 1 PRO A 128 -158.68 -77.05 REMARK 500 2 PRO A 46 95.17 -43.68 REMARK 500 2 GLN A 47 80.13 -151.81 REMARK 500 2 ASP A 79 101.66 -53.48 REMARK 500 2 ASN A 82 -62.28 -121.10 REMARK 500 2 THR A 83 -22.07 76.90 REMARK 500 2 PRO A 113 90.79 -64.74 REMARK 500 2 LEU A 129 101.09 -53.63 REMARK 500 3 ASP A 48 89.50 -67.69 REMARK 500 3 LYS A 49 -48.90 -151.67 REMARK 500 3 THR A 83 -19.23 77.38 REMARK 500 3 GLU A 115 141.05 -172.64 REMARK 500 3 LEU A 129 99.62 -63.92 REMARK 500 4 LYS A 49 -63.26 -122.01 REMARK 500 4 HIS A 51 59.04 -143.25 REMARK 500 4 SER A 84 66.32 60.65 REMARK 500 5 PRO A 46 92.16 -58.60 REMARK 500 5 GLN A 47 39.59 -87.68 REMARK 500 6 GLN A 47 89.70 -64.49 REMARK 500 6 HIS A 51 79.22 -67.83 REMARK 500 6 PRO A 113 109.69 -57.51 REMARK 500 7 PRO A 46 105.44 -53.29 REMARK 500 7 PRO A 128 -165.96 -75.40 REMARK 500 7 LEU A 129 99.05 -66.41 REMARK 500 8 PRO A 113 95.28 -60.66 REMARK 500 9 PRO A 46 -152.65 -98.27 REMARK 500 9 PRO A 113 88.14 -61.02 REMARK 500 9 LEU A 129 91.14 -67.33 REMARK 500 10 ASN A 82 50.23 -102.41 REMARK 500 11 ALA A 44 28.10 -161.56 REMARK 500 11 THR A 45 123.80 57.91 REMARK 500 11 PRO A 101 99.87 -67.08 REMARK 500 12 ASP A 48 31.20 -84.63 REMARK 500 12 ALA A 70 147.96 -173.96 REMARK 500 12 PRO A 101 96.80 -62.33 REMARK 500 13 PRO A 46 174.54 -55.85 REMARK 500 13 PRO A 101 102.63 -55.39 REMARK 500 13 PRO A 113 89.34 -65.49 REMARK 500 14 THR A 45 86.65 55.96 REMARK 500 14 GLN A 47 37.65 -149.30 REMARK 500 14 PRO A 113 97.09 -48.92 REMARK 500 14 LEU A 129 29.77 -165.44 REMARK 500 15 PRO A 128 -82.39 -67.97 REMARK 500 16 PRO A 46 97.72 -58.89 REMARK 500 16 LEU A 67 35.61 -86.30 REMARK 500 16 ASP A 68 -84.94 26.42 REMARK 500 16 PRO A 101 107.79 -57.98 REMARK 500 REMARK 500 THIS ENTRY HAS 62 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: DVR115G RELATED DB: TARGETDB DBREF 2KCT A 44 128 UNP Q72D78 Q72D78_DESVH 44 128 SEQADV 2KCT MET A 43 UNP Q72D78 EXPRESSION TAG SEQADV 2KCT LEU A 129 UNP Q72D78 EXPRESSION TAG SEQADV 2KCT GLU A 130 UNP Q72D78 EXPRESSION TAG SEQADV 2KCT HIS A 131 UNP Q72D78 EXPRESSION TAG SEQADV 2KCT HIS A 132 UNP Q72D78 EXPRESSION TAG SEQADV 2KCT HIS A 133 UNP Q72D78 EXPRESSION TAG SEQADV 2KCT HIS A 134 UNP Q72D78 EXPRESSION TAG SEQADV 2KCT HIS A 135 UNP Q72D78 EXPRESSION TAG SEQADV 2KCT HIS A 136 UNP Q72D78 EXPRESSION TAG SEQRES 1 A 94 MET ALA THR PRO GLN ASP LYS LEU HIS THR VAL ARG LEU SEQRES 2 A 94 PHE GLY THR VAL ALA ALA ASP GLY LEU THR MET LEU ASP SEQRES 3 A 94 GLY ALA PRO GLY VAL ARG PHE ARG LEU GLU ASP LYS ASP SEQRES 4 A 94 ASN THR SER LYS THR VAL TRP VAL LEU TYR LYS GLY ALA SEQRES 5 A 94 VAL PRO ASP THR PHE LYS PRO GLY VAL GLU VAL ILE ILE SEQRES 6 A 94 GLU GLY GLY LEU ALA PRO GLY GLU ASP THR PHE LYS ALA SEQRES 7 A 94 ARG THR LEU MET THR LYS CYS PRO LEU GLU HIS HIS HIS SEQRES 8 A 94 HIS HIS HIS SHEET 1 A 7 THR A 65 MET A 66 0 SHEET 2 A 7 GLY A 72 GLU A 78 -1 O ARG A 74 N THR A 65 SHEET 3 A 7 THR A 86 LYS A 92 -1 O VAL A 87 N LEU A 77 SHEET 4 A 7 THR A 117 THR A 125 1 O PHE A 118 N LEU A 90 SHEET 5 A 7 GLU A 104 LEU A 111 -1 N ILE A 106 O MET A 124 SHEET 6 A 7 VAL A 53 VAL A 59 -1 N VAL A 53 O GLY A 109 SHEET 7 A 7 GLY A 72 GLU A 78 -1 O GLU A 78 N THR A 58 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