HEADER DNA BINDING PROTEIN 30-JUN-08 2K5V TITLE SOLUTION NMR STRUCTURE OF THE SECOND OB-FOLD DOMAIN OF REPLICATION TITLE 2 PROTEIN A FROM METHANOCOCCUS MARIPALUDIS. NORTHEAST STRUCTURAL TITLE 3 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 DOMAIN, KEYWDS 2 STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NORTHEAST KEYWDS 3 STRUCTURAL GENOMICS CONSORTIUM, NESG, 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,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 6 08-MAY-24 2K5V 1 REMARK REVDAT 5 14-JUN-23 2K5V 1 REMARK REVDAT 4 20-OCT-21 2K5V 1 SEQADV REVDAT 3 19-FEB-20 2K5V 1 REMARK SEQADV 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,R.NAIR, JRNL AUTH 2 J.K.EVERETT,G.VT.SWAPNA,T.B.ACTON,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE SECOND OB-FOLD DOMAIN OF JRNL TITL 2 REPLICATION PROTEIN A FROM METHANOCOCCUS MARIPALUDIS. JRNL TITL 3 NORTHEAST STRUCTURAL GENOMICS TARGET MRR110B. JRNL REF TO BE PUBLISHED JRNL REFN 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 DISTANCE REMARK 3 CONSTRAINTS AND 125 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND REMARK 3 CONSTRAINTS (18.5 CONSTRAINTS PER RESIDUE, 6.2 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 172 TO 269 BY REMARK 3 PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY REMARK 3 USING CYANA 2.1. 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 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 DEPOSITION ID IS D_1000100714. 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% 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, 100% D2O; 0.94 MM REMARK 210 [U-5% 13C; U-100% 15N] MRR110B, REMARK 210 20 MM MES, 100 MM SODIUM REMARK 210 CHLORIDE, 5 MM CALCIUM CHLORIDE, REMARK 210 10 MM DTT, 0.02 % SODIUM AZIDE, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HN(CA)CO; 3D CBCA(CO) REMARK 210 NH; 3D HNCACB; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-COSY ALIPHATIC; 3D HCCH- REMARK 210 TOCSY ALIPHATIC; 3D CCH-TOCSY REMARK 210 ALIPHATIC; 3D HNHA; 3D REMARK 210 SIMULTANEOUS CN NOESY; 3D 1H-13C REMARK 210 NOESY AROMATIC; 2D 1H-13C HSQC REMARK 210 HIGH RES. (L/V STEREOASSIGNMENT); REMARK 210 2D 1H-15N HETNOE; 2D 1H-15N T1/ REMARK 210 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 2.4.0, REMARK 210 NMRPIPE 2.3, CYANA 2.1, CNS 1.2, REMARK 210 SPARKY 3.113, AUTOSTRUCTURE REMARK 210 2.2.1, PSVS 1.3, 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 REMARK 210 BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND REMARK 210 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING REMARK 210 TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE REMARK 210 ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN REMARK 210 ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY REMARK 210 ASSIGNMENTS WERE DETERMINED USING CYANA 2.1. 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, 100%, SIDE CHAIN, 99.7%, REMARK 210 AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC REMARK 210 SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR REMARK 210 RESIDUES 172 TO 269, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) REMARK 210 + S(PSI) > 1.8] COMPRISE: 173-204,209-249,254-265: (A) RMSD REMARK 210 (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.0. (B) RAMACHANDRAN REMARK 210 STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 92.4%, REMARK 210 ADDITIONALLY ALLOWED, 6.6%, GENEROUSLY ALLOWED, 1.0%, REMARK 210 DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES REMARK 210 (RAW/Z-): PHI-PSI, -0.60/-2.05, ALL, -0.36/-2.13. (D) REMARK 210 MOLPROBITY CLASH SCORE (RAW/Z-): 16.29/-1.27 (E) RPF SCORES REMARK 210 FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 172-269): RECALL, REMARK 210 0.990, PRECISION, 0.933, F-MEASURE, 0.961, DP-SCORE, 0.836. REMARK 210 (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. THE C-TERMINAL REMARK 210 HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN REMARK 210 THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS REMARK 210 DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT REMARK 210 WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 172,205-208,250-253, REMARK 210 266-269. 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 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 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 REMARK 500 THIS ENTRY HAS 59 RAMACHANDRAN OUTLIERS. 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 MUTATION 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 MODEL 1