10 20 30 40 50 60 70 80 2K5V - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA BINDING PROTEIN 30-JUN-08 2K5V
TITLE SOLUTION NMR STRUCTURE OF THE SECOND OB-FOLD DOMAIN OF TITLE 2 REPLICATION PROTEIN A FROM METHANOCOCCUS MARIPALUDIS. TITLE 3 NORTHEAST STRUCTURAL GENOMICS TARGET MRR110B.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICATION PROTEIN A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCOCCUS MARIPALUDIS; SOURCE 3 ORGANISM_TAXID: 39152; SOURCE 4 GENE: RPA, MMP1032; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: MRR110B-21.1
KEYWDS SOLUTION NMR STRUCTURE, REPLICATION PROTEIN A, OB-FOLD KEYWDS 2 DOMAIN, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, KEYWDS 4 DNA BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR J.M.ARAMINI,M.MAGLAQUI,M.JIANG,C.CICCOSANTI,R.XIAO,R.NAIR, AUTHOR 2 J.K.EVERETT,G.VT.SWAPNA,T.B.ACTON,B.ROST,G.T.MONTELIONE, AUTHOR 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)
REVDAT 2 24-FEB-09 2K5V 1 VERSN REVDAT 1 19-AUG-08 2K5V 0
JRNL AUTH J.M.ARAMINI,M.MAGLAQUI,M.JIANG,C.CICCOSANTI,R.XIAO, JRNL AUTH 2 R.NAIR,J.K.EVERETT,G.VT.SWAPNA,T.B.ACTON, JRNL AUTH 3 G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE SECOND OB-FOLD JRNL TITL 2 DOMAIN OF REPLICATION PROTEIN A FROM METHANOCOCCUS JRNL TITL 3 MARIPALUDIS. NORTHEAST STRUCTURAL GENOMICS TARGET JRNL TITL 4 MRR110B. JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 1692 CONFORMATIONALLY-RESTRICTING NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS AND 125 DIHEDRAL ANGLE CONSTRAINTS; 0 REMARK 3 HYDROGEN BOND CONSTRAINTS (18.5 CONSTRAINTS PER RESIDUE, 6.2 REMARK 3 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 172 REMARK 3 TO 269 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED REMARK 3 ITERATIVELY USING CYANA 2.1. THE 20 STRUCTURES OUT OF 100 WITH REMARK 3 THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED REMARK 3 MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) REMARK 3 WITH PARAM19.
REMARK 4 REMARK 4 2K5V COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-08. REMARK 100 THE RCSB ID CODE IS RCSB100714.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.18 MM [U-100% 13C 15N] REMARK 210 MRR110B, 20 MM MES, 100 MM REMARK 210 SODIUM CHLORIDE, 5 MM CALCIUM REMARK 210 CHLORIDE, 10 MM DTT, 0.02 % REMARK 210 SODIUM AZIDE, 95% H2O/ 5% D2O; REMARK 210 1.18 MM [U-100% 13C; U -100% REMARK 210 15N] MRR110B, 20 MM MES, 100 REMARK 210 MM SODIUM CHLORIDE, 5 MM REMARK 210 CALCIUM CHLORIDE, 10 MM DTT, REMARK 210 0.02 % SODIUM AZIDE, 100% D2O; REMARK 210 0.94 MM [U-5% 13C; U-100% 15N] REMARK 210 MRR110B, 20 MM MES, 100 MM REMARK 210 SODIUM CHLORIDE, 5 MM CALCIUM REMARK 210 CHLORIDE, 10 MM DTT, 0.02 % REMARK 210 SODIUM AZIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC, 2D 1H-13C REMARK 210 HSQC, 3D HNCO, 3D HN(CA)CO, 3D REMARK 210 CBCA(CO)NH, 3D HNCACB, 3D REMARK 210 HBHA(CO)NH, 3D HCCH-COSY REMARK 210 ALIPHATIC, 3D HCCH-TOCSY REMARK 210 ALIPHATIC, 3D CCH-TOCSY REMARK 210 ALIPHATIC, 3D HNHA, 3D REMARK 210 SIMULTANEOUS CN NOESY, 3D 1H- REMARK 210 13C NOESY AROMATIC, 2D 1H-13C REMARK 210 HSQC HIGH RES. (L/V REMARK 210 STEREOASSIGNMENT), 2D 1H-15N REMARK 210 HETNOE, 2D 1H-15N T1/T2 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 : TOPSPIN 2.1, AUTOASSIGN REMARK 210 2.4.0, NMRPIPE 2.3, CYANA 2.1, REMARK 210 CNS 1.2, SPARKY 3.113, REMARK 210 AUTOSTRUCTURE 2.2.1, PSVS 1.3, REMARK 210 PDBSTAT 5.0 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 THE SIDE CHAIN ASSIGNMENTS REMARK 210 WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE REMARK 210 DETERMINED USING CYANA 2.1. BACKBONE (PHI/ PSI) DIHEDRAL ANGLE REMARK 210 CONSTRAINTS WERE OBTAINED FROM TALOS. ROTAMER STATES OF REMARK 210 SPECIFIC ORDERED RESIDUES WERE CONSTRAINED IN THE FINAL STAGE REMARK 210 OF THE STRUCTURE REFINEMENT BASED ON PROCHECK. COMPLETENESS OF REMARK 210 NMR ASSIGNMENTS (EXCLUDING C- TERMINAL HHHHHH): BACKBONE, 100% REMARK 210 , SIDE CHAIN, 99.7%, AROMATICS, 100%, STEREOSPECIFIC METHYL, REMARK 210 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE REMARK 210 QUALITY FACTORS (FOR RESIDUES 172 TO 269, PSVS 1.3), WHERE REMARK 210 ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 173-204, REMARK 210 209-249,254-265: (A) RMSD (ORDERED RESIDUES): BB, 0.6, HEAVY REMARK 210 ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: REMARK 210 MOST FAVORED, 92.4%, ADDITIONALLY ALLOWED, 6.6%, GENEROUSLY REMARK 210 ALLOWED, 1.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR REMARK 210 ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.60/-2.05, ALL, -0.36/- REMARK 210 2.13. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 16.29/-1.27 (E) RPF REMARK 210 SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 172-269): REMARK 210 RECALL, 0.990, PRECISION, 0.933, F-MEASURE, 0.961, DP-SCORE, REMARK 210 0.836. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. 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]: 172,205-208, REMARK 210 250-253, 266-269.
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 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 270 REMARK 465 HIS A 271 REMARK 465 HIS A 272 REMARK 465 HIS A 273 REMARK 465 HIS A 274 REMARK 465 HIS A 275
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 ASN A 228 -134.24 52.93 REMARK 500 2 ASP A 217 -164.85 -116.44 REMARK 500 2 ASN A 228 -134.27 60.80 REMARK 500 2 GLU A 234 92.98 -67.84 REMARK 500 3 ASN A 228 -141.68 57.83 REMARK 500 3 GLU A 234 87.82 -68.39 REMARK 500 3 SER A 252 -17.65 155.75 REMARK 500 4 ASN A 228 -138.03 66.83 REMARK 500 4 GLU A 234 96.57 -63.29 REMARK 500 4 LYS A 237 99.96 -68.02 REMARK 500 5 ASN A 228 -141.16 58.87 REMARK 500 6 VAL A 192 -64.77 -90.41 REMARK 500 6 ARG A 202 -167.73 -100.09 REMARK 500 6 LYS A 211 119.45 -162.05 REMARK 500 6 ASN A 228 -134.29 54.95 REMARK 500 7 PRO A 196 -164.65 -70.28 REMARK 500 7 ASN A 228 -134.13 56.08 REMARK 500 7 LYS A 237 95.82 -66.27 REMARK 500 8 ASP A 204 70.98 -106.17 REMARK 500 8 THR A 206 -175.85 52.23 REMARK 500 8 ASN A 228 -132.52 51.01 REMARK 500 8 GLU A 234 99.40 -66.86 REMARK 500 8 ILE A 264 -74.52 -77.10 REMARK 500 9 LEU A 179 98.86 -64.45 REMARK 500 9 ASN A 228 -141.11 55.72 REMARK 500 10 LYS A 211 115.20 -167.38 REMARK 500 10 ASN A 228 -133.54 58.48 REMARK 500 10 GLU A 234 97.36 -62.86 REMARK 500 10 LYS A 237 94.77 -69.35 REMARK 500 11 ASN A 228 -152.25 62.18 REMARK 500 11 GLU A 229 -7.29 -58.62 REMARK 500 11 TYR A 251 108.46 -59.68 REMARK 500 11 LEU A 268 79.99 -119.97 REMARK 500 12 PRO A 196 -174.83 -57.67 REMARK 500 12 ASN A 228 -143.36 64.08 REMARK 500 12 SER A 252 85.66 -59.81 REMARK 500 12 LEU A 268 -32.59 -137.59 REMARK 500 13 ASN A 228 -150.97 61.94 REMARK 500 13 PHE A 233 103.03 -50.87 REMARK 500 13 SER A 267 63.18 66.87 REMARK 500 14 ASN A 228 -155.39 63.76 REMARK 500 15 PRO A 196 162.07 -49.46 REMARK 500 15 ASN A 228 -133.93 57.69 REMARK 500 16 ASN A 228 -146.84 61.51 REMARK 500 16 GLU A 234 90.61 -68.85 REMARK 500 16 LEU A 268 -29.85 -154.33 REMARK 500 17 ASN A 228 -153.60 57.89 REMARK 500 17 LYS A 237 109.24 -42.99 REMARK 500 17 SER A 252 -51.99 73.81 REMARK 500 17 LYS A 266 80.94 -69.04 REMARK 500 18 ASN A 182 33.68 70.52 REMARK 500 18 ASN A 228 -141.88 58.60 REMARK 500 18 TYR A 251 97.30 -63.27 REMARK 500 18 SER A 257 93.81 -64.77 REMARK 500 19 THR A 206 -144.16 -86.06 REMARK 500 19 ASN A 228 -132.57 56.75 REMARK 500 19 SER A 252 -27.42 68.66 REMARK 500 20 ASN A 228 -128.30 53.00 REMARK 500 20 LYS A 237 93.91 -67.91 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MRR110B RELATED DB: TARGETDB REMARK 900 RELATED ID: 15849 RELATED DB: BMRB
DBREF 2K5V A 173 267 UNP Q6LYF9 Q6LYF9_METMP 173 267
SEQADV 2K5V MET A 172 UNP Q6LYF9 EXPRESSION TAG SEQADV 2K5V ALA A 193 UNP Q6LYF9 THR 193 ENGINEERED SEQADV 2K5V LEU A 268 UNP Q6LYF9 EXPRESSION TAG SEQADV 2K5V GLU A 269 UNP Q6LYF9 EXPRESSION TAG SEQADV 2K5V HIS A 270 UNP Q6LYF9 EXPRESSION TAG SEQADV 2K5V HIS A 271 UNP Q6LYF9 EXPRESSION TAG SEQADV 2K5V HIS A 272 UNP Q6LYF9 EXPRESSION TAG SEQADV 2K5V HIS A 273 UNP Q6LYF9 EXPRESSION TAG SEQADV 2K5V HIS A 274 UNP Q6LYF9 EXPRESSION TAG SEQADV 2K5V HIS A 275 UNP Q6LYF9 EXPRESSION TAG
SEQRES 1 A 104 MET ASN TYR LYS ILE SER GLU LEU MET PRO ASN LEU SER SEQRES 2 A 104 GLY THR ILE ASN ALA GLU VAL VAL ALA ALA TYR PRO LYS SEQRES 3 A 104 LYS GLU PHE SER ARG LYS ASP GLY THR LYS GLY GLN LEU SEQRES 4 A 104 LYS SER LEU PHE LEU LYS ASP ASP THR GLY SER ILE ARG SEQRES 5 A 104 GLY THR LEU TRP ASN GLU LEU ALA ASP PHE GLU VAL LYS SEQRES 6 A 104 LYS GLY ASP ILE ALA GLU VAL SER GLY TYR VAL LYS GLN SEQRES 7 A 104 GLY TYR SER GLY LEU GLU ILE SER VAL ASP ASN ILE GLY SEQRES 8 A 104 ILE ILE GLU LYS SER LEU GLU HIS HIS HIS HIS HIS HIS
HELIX 1 1 LYS A 175 LEU A 179 5 5 HELIX 2 2 GLU A 229 PHE A 233 5 5
SHEET 1 A 6 LEU A 183 SER A 201 0 SHEET 2 A 6 LYS A 207 ASP A 217 -1 O GLY A 208 N PHE A 200 SHEET 3 A 6 GLY A 220 TRP A 227 -1 O ILE A 222 N LEU A 215 SHEET 4 A 6 GLY A 253 ILE A 263 1 O VAL A 258 N THR A 225 SHEET 5 A 6 ILE A 240 GLY A 250 -1 N SER A 244 O ASN A 260 SHEET 6 A 6 LEU A 183 SER A 201 -1 N LEU A 183 O VAL A 247
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