HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 13-SEP-10 2L3F TITLE SOLUTION NMR STRUCTURE OF A PUTATIVE URACIL DNA GLYCOSYLASE FROM TITLE 2 METHANOSARCINA ACETIVORANS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 3 TARGET MVR76 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA ACETIVORANS; SOURCE 3 ORGANISM_TAXID: 2214; SOURCE 4 GENE: MA_0462; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PMGK; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET21 KEYWDS STRUCTURAL GENOMICS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), KEYWDS 2 PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, UNKNOWN FUNCTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,K.HAMILTON,C.T.CICCOSANTI,H.WANG,H.W.LEE,B.ROST, AUTHOR 2 T.B.ACTON,R.XIAO,J.K.EVERETT,G.T.MONTELIONE,NORTHEAST STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (NESG) REVDAT 3 01-MAY-24 2L3F 1 REMARK SEQADV REVDAT 2 22-FEB-12 2L3F 1 VERSN KEYWDS REVDAT 1 20-OCT-10 2L3F 0 JRNL AUTH J.M.ARAMINI,K.HAMILTON,C.T.CICCOSANTI,H.WANG,H.W.LEE,B.ROST, JRNL AUTH 2 T.B.ACTON,R.XIAO,J.K.EVERETT,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF A PUTATIVE URACIL DNA GLYCOSYLASE JRNL TITL 2 FROM METHANOSARCINA ACETIVORANS, NORTHEAST STRUCTURAL JRNL TITL 3 GENOMICS CONSORTIUM TARGET MVR76 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, CYANA 3.0 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 2729 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS AND 234 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND REMARK 3 CONSTRAINTS (18.4 CONSTRAINTS PER RESIDUE, 5.4 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 161 BY PSVS REMARK 3 1.4). IN ADDITION, 210 RESOLVED N-H RESIDUAL DIPOLAR COUPLINGS REMARK 3 FOR ORDERED RESIDUES OBTAINED FROM TWO ALIGNMENTS WERE INCLUDED REMARK 3 IN ALL STRUCTURE CALCULATIONS. STRUCTURE DETERMINATION WAS REMARK 3 PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF REMARK 3 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY REMARK 3 RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT REMARK 3 WATER (CNS) WITH PARAM19. REMARK 4 REMARK 4 2L3F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000101907. 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 : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.94 MM [U-100% 13C; U-100% 15N] REMARK 210 MVR76, 20 MM MES, 100 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; 1.15 REMARK 210 MM [U-5% 13C; U-100% 15N] MVR76, 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 50 UM DSS, 90% H2O/10% D2O; 0.80 REMARK 210 MM [U-5% 13C; U-100% 15N] MVR76, 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 50 UM DSS, 4 % C12E5 PEG, 90% REMARK 210 H2O/10% D2O; 1.15 MM [U-5% 13C; REMARK 210 U-100% 15N] MVR76, 20 MM MES, REMARK 210 100 MM SODIUM CHLORIDE, 5 MM REMARK 210 CALCIUM CHLORIDE, 10 MM DTT, REMARK 210 0.02 % SODIUM AZIDE, 50 UM DSS, REMARK 210 7 % POLYACRYLAMIDE GEL, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-13C HSQC HIGH REMARK 210 RESOLUTION (L/V METHYL REMARK 210 STEREOASSIGNMENT); 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 CCH-TOCSY; 3D HCCH-COSY; 3D HNHA; REMARK 210 3D HBHANH; 1D 15N T1 AND T2; 2D REMARK 210 1H-15N HETNOE; NH J-MODULATION 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 : CYANA 3.0, AUTOSTRUCTURE 2.2.1, REMARK 210 PSVS 1.4, NMRPIPE 2.3, REMARK 210 MOLPROBITY 3.18, TOPSPIN 2.1, REMARK 210 PDBSTAT 5.1, PINE 1.0, SPARKY REMARK 210 3.112, TALOS+, PALES, VNMRJ 2.1 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 CHROMATOGRAPHY, REMARK 210 STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE REMARK 210 WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA REMARK 210 FOR BACKBONE AND SIDE CHAIN ASSIGNMENTS WERE OBTAINED ON A 1.7- REMARK 210 MM MICROCRYOPROBE AT 600 MHZ. ALL NOESY DATA WERE ACQUIRED AT REMARK 210 800 MHZ USING A 5-MM CROYOPROBE. BACKBONE ASSIGNMENTS WERE MADE REMARK 210 USING PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED REMARK 210 MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING REMARK 210 CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE REMARK 210 OBTAINED FROM TALOSPLUS. COMPLETENESS OF NMR ASSIGNMENTS REMARK 210 (EXCLUDING C-TERMINAL HIS5): BACKBONE, 98.5%, SIDE CHAIN, 91.0%, REMARK 210 AROMATICS, 84.3%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC REMARK 210 SIDE CHAIN NH2: 64.0%. FINAL STRUCTURE QUALITY FACTORS (FOR REMARK 210 RESIDUES 1 TO 161, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + REMARK 210 S(PSI) > 1.8] COMPRISE: 2-34,39-81,92-144,146-160: (A) RMSD REMARK 210 (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.1. (B) RAMACHANDRAN REMARK 210 STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 89.1%, REMARK 210 ADDITIONALLY ALLOWED, 10.8%, GENEROUSLY ALLOWED, 0.0%, REMARK 210 DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/ REMARK 210 Z-): PHI-PSI, -0.26/-0.71, ALL, -0.15/-0.89. (D) MOLPROBITY REMARK 210 CLASH SCORE (RAW/Z-): 16.95/-1.38 (E) RPF SCORES FOR GOODNESS OF REMARK 210 FIT TO NOESY DATA (RESIDUES 1 TO 161): RECALL, 0.951, PRECISION, REMARK 210 0.899, F-MEASURE, 0.924, DP-SCORE, 0.722. (F) NUMBER OF CLOSE REMARK 210 CONTACTS PER 20 MODELS: 11. THE FINAL FIVE HISTIDINE RESIDUES IN REMARK 210 THE C-TERMINAL AFFINITY TAG WERE NOT INCLUDED IN THE STRUCTURE REMARK 210 CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. 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 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 REMARK 465 HIS A 166 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 21 -82.17 -89.61 REMARK 500 1 PRO A 37 0.56 -66.07 REMARK 500 1 TRP A 73 -168.96 -165.09 REMARK 500 1 ASP A 91 133.41 -38.88 REMARK 500 1 GLU A 160 -62.52 -98.48 REMARK 500 2 SER A 21 -75.59 -89.81 REMARK 500 2 TRP A 73 -169.14 -165.29 REMARK 500 2 ASP A 86 -24.82 73.24 REMARK 500 2 SER A 145 30.08 -86.85 REMARK 500 2 LYS A 146 -70.57 -67.71 REMARK 500 3 SER A 21 -71.78 -94.64 REMARK 500 3 TRP A 73 -169.16 -162.62 REMARK 500 3 GLU A 82 -72.92 -134.51 REMARK 500 3 ASP A 86 -72.44 66.57 REMARK 500 3 ASP A 91 148.98 -170.42 REMARK 500 4 SER A 21 -78.55 -93.94 REMARK 500 4 ASN A 52 99.82 -68.30 REMARK 500 4 ASP A 86 77.39 -56.09 REMARK 500 4 SER A 87 16.80 56.04 REMARK 500 4 SER A 137 49.12 -86.34 REMARK 500 4 SER A 145 34.98 -157.32 REMARK 500 5 VAL A 9 58.24 -91.03 REMARK 500 5 ASN A 13 77.64 -103.43 REMARK 500 5 SER A 21 -72.46 -103.99 REMARK 500 5 ASN A 52 93.07 -66.27 REMARK 500 5 TRP A 73 -168.90 -165.88 REMARK 500 5 ASP A 86 -38.62 79.52 REMARK 500 5 ASP A 91 154.56 179.05 REMARK 500 5 ARG A 108 -28.93 -142.64 REMARK 500 5 SER A 137 36.34 -79.33 REMARK 500 6 SER A 21 -68.54 -100.38 REMARK 500 6 LEU A 107 104.12 -58.67 REMARK 500 6 LYS A 146 -74.21 -72.39 REMARK 500 7 SER A 21 -89.96 -90.57 REMARK 500 7 ASN A 52 88.73 -68.47 REMARK 500 7 TRP A 73 -168.07 -161.80 REMARK 500 7 SER A 84 -157.69 -83.31 REMARK 500 7 ASP A 91 146.68 -178.78 REMARK 500 8 VAL A 9 47.86 -92.40 REMARK 500 8 SER A 21 -82.02 -87.77 REMARK 500 8 GLN A 85 68.10 -109.98 REMARK 500 8 ASP A 91 158.31 176.48 REMARK 500 8 LEU A 107 107.97 -59.28 REMARK 500 8 SER A 145 70.95 -169.37 REMARK 500 9 VAL A 9 72.86 -100.03 REMARK 500 9 SER A 21 -71.43 -100.43 REMARK 500 9 GLN A 31 18.24 56.16 REMARK 500 9 SER A 84 -44.61 -158.76 REMARK 500 9 SER A 87 -160.22 -168.73 REMARK 500 9 ARG A 108 -34.50 -136.68 REMARK 500 REMARK 500 THIS ENTRY HAS 118 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MVR76 RELATED DB: TARGETDB DBREF 2L3F A 1 158 UNP Q8TTH3 Q8TTH3_METAC 1 158 SEQADV 2L3F LEU A 159 UNP Q8TTH3 EXPRESSION TAG SEQADV 2L3F GLU A 160 UNP Q8TTH3 EXPRESSION TAG SEQADV 2L3F HIS A 161 UNP Q8TTH3 EXPRESSION TAG SEQADV 2L3F HIS A 162 UNP Q8TTH3 EXPRESSION TAG SEQADV 2L3F HIS A 163 UNP Q8TTH3 EXPRESSION TAG SEQADV 2L3F HIS A 164 UNP Q8TTH3 EXPRESSION TAG SEQADV 2L3F HIS A 165 UNP Q8TTH3 EXPRESSION TAG SEQADV 2L3F HIS A 166 UNP Q8TTH3 EXPRESSION TAG SEQRES 1 A 166 MET ILE LYS ARG GLY PHE PRO ALA VAL LEU ASP GLU ASN SEQRES 2 A 166 THR GLU ILE LEU ILE LEU GLY SER LEU PRO SER ASP GLU SEQRES 3 A 166 SER ILE ARG LYS GLN GLN TYR TYR GLY ASN PRO GLY ASN SEQRES 4 A 166 ASP PHE TRP ARG LEU VAL GLY HIS ALA ILE GLY GLU ASN SEQRES 5 A 166 LEU GLN ASP MET ALA TYR GLU LYS LYS LEU LYS THR LEU SEQRES 6 A 166 LYS HIS ASN ARG ILE GLY LEU TRP ASP VAL PHE LYS ALA SEQRES 7 A 166 GLY SER ARG GLU GLY SER GLN ASP SER LYS ILE GLY ASP SEQRES 8 A 166 GLU GLU ILE ASN ASP PHE SER GLY LEU LYS GLU MET VAL SEQRES 9 A 166 PRO LYS LEU ARG LEU ILE CYS PHE ASN GLY ARG LYS ALA SEQRES 10 A 166 GLY GLU TYR GLU PRO LEU LEU ARG GLY MET GLY TYR GLU SEQRES 11 A 166 THR LYS VAL LEU PRO SER SER SER GLY ALA ASN ARG ARG SEQRES 12 A 166 PHE SER LYS ASN ARG GLU SER GLU TRP GLU ALA VAL PHE SEQRES 13 A 166 ARG HIS LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 SER A 24 GLN A 31 1 8 HELIX 2 2 GLN A 32 ASN A 36 5 5 HELIX 3 3 ASP A 40 GLY A 50 1 11 HELIX 4 4 ALA A 57 ASN A 68 1 12 HELIX 5 5 GLY A 99 VAL A 104 1 6 HELIX 6 6 GLY A 114 GLU A 119 1 6 HELIX 7 7 TYR A 120 ARG A 125 1 6 HELIX 8 8 GLY A 126 GLY A 128 5 3 HELIX 9 9 SER A 138 ARG A 143 1 6 HELIX 10 10 ARG A 148 ARG A 157 1 10 HELIX 11 11 HIS A 158 GLU A 160 5 3 SHEET 1 A 3 LYS A 3 ARG A 4 0 SHEET 2 A 3 PHE A 76 GLY A 79 -1 O GLY A 79 N LYS A 3 SHEET 3 A 3 GLU A 93 ILE A 94 -1 O GLU A 93 N ALA A 78 SHEET 1 B 4 ILE A 70 ASP A 74 0 SHEET 2 B 4 ILE A 16 GLY A 20 1 N ILE A 18 O GLY A 71 SHEET 3 B 4 LEU A 109 ASN A 113 1 O ASN A 113 N LEU A 19 SHEET 4 B 4 GLU A 130 LEU A 134 1 O LYS A 132 N PHE A 112 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