HEADER TRANSFERASE 07-MAY-09 2KIM TITLE 1.7-MM MICROCRYOPROBE SOLUTION NMR STRUCTURE OF AN O6-METHYLGUANINE TITLE 2 DNA METHYLTRANSFERASE FAMILY PROTEIN FROM VIBRIO PARAHAEMOLYTICUS. TITLE 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET VPR247. COMPND MOL_ID: 1; COMPND 2 MOLECULE: O6-METHYLGUANINE-DNA METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: METHYLATED-DNA-PROTEIN-CYSTEINE METHYLTRANSFERASE-RELATED COMPND 5 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARAHAEMOLYTICUS AQ3810; SOURCE 3 ORGANISM_TAXID: 419109; SOURCE 4 GENE: A79_1377, VP0951; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)MGK; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: VPR247-21.9 KEYWDS METHODS DEVELOPMENT, SOLUTION NMR STRUCTURE, DNA BASE REPAIR, O6 KEYWDS 2 METHYLGUANINE METHYLTRANSFERASE, NESG, PSI-2, METHYLTRANSFERASE, KEYWDS 3 TRANSFERASE, STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, KEYWDS 4 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,R.L.BELOTE,C.T.CICCOSANTI,M.JIANG,B.ROST,R.NAIR, AUTHOR 2 G.V.T.SWAPNA,T.B.ACTON,R.XIAO,J.K.EVERETT,G.T.MONTELIONE,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 2 31-JAN-18 2KIM 1 AUTHOR REMARK REVDAT 1 07-JUL-09 2KIM 0 JRNL AUTH J.M.ARAMINI,R.L.BELOTE,C.T.CICCOSANTI,M.JIANG,B.ROST,R.NAIR, JRNL AUTH 2 G.V.T.SWAPNA,T.B.ACTON,R.XIAO,J.K.EVERETT,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF AN O6-METHYLGUANINE DNA JRNL TITL 2 METHYLTRANSFERASE FAMILY PROTEIN FROM VIBRIO JRNL TITL 3 PARAHAEMOLYTICUS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM JRNL TITL 4 TARGET VPR247. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, CNS 1.2 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 1835 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS, 117 DIHEDRAL ANGLE CONSTRAINTS, AND 56 HYDROGEN REMARK 3 BOND CONSTRAINTS (19.9 CONSTRAINTS PER RESIDUE, 5.4 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 102 BY PSVS REMARK 3 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING REMARK 3 CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET REMARK 3 FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ REMARK 3 ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19, AND REMARK 3 USING NEUTRAL HISTIDINES (NE2H TAUTOMER) AT POSITIONS 13 AND 38. REMARK 4 REMARK 4 2KIM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000101166. 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 : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.94 MM [U-100% 13C; U-100% 15N] REMARK 210 VPR247, 20 MM MES, 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; 0.92 REMARK 210 MM [U-5% 13C; U-100% 15N] VPR247, REMARK 210 20 MM MES, 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 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HNCA; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-COSY ALIPHATIC; 3D HCCH- REMARK 210 TOCSY ALIPHATIC; 3D (H)CCH-TOCSY REMARK 210 ALIPHATIC; 3D HNHA; 3D HN(CO)CA; REMARK 210 2D 1H-15N HETNOE; 1D 1H-15N T1 REMARK 210 AND T2; 2D 1H-13C HSQC HIGH RES. REMARK 210 (L/V METHYL STEREOASSIGNMENT); REMARK 210 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 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, NMRPIPE 2.3, SPARKY REMARK 210 3.112, PINE 1.0, AUTOASSIGN REMARK 210 2.4.0, CYANA 3.0, AUTOSTRUCTURE REMARK 210 2.2.1, PSVS 1.3, MOLPROBITY 3.15, REMARK 210 PDBSTAT 5.1 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 AND NOESY SPECTRA USED REMARK 210 FOR STRUCTURE CALCULATION WERE OBTAINED ON A 1.7-MM REMARK 210 MICROCRYOPROBE AT 600 MHZ. BACKBONE ASSIGNMENTS WERE MADE USING REMARK 210 AUTOASSIGN AND PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE REMARK 210 COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED REMARK 210 USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS REMARK 210 WERE OBTAINED FROM TALOS. HYDROGEN BOND CONSTRAINTS WERE REMARK 210 DETERMINED USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED REMARK 210 ONLY IN THE FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE REMARK 210 DETERMINATION. ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE REMARK 210 CONSTRAINED IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED REMARK 210 ON PROCHECK AND MOLPROBITY. COMPLETENESS OF NMR ASSIGNMENTS REMARK 210 (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 97.6%, SIDE CHAIN, 98.3% REMARK 210 , AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC REMARK 210 SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR REMARK 210 RESIDUES 1 TO 102, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + REMARK 210 S(PSI) > 1.8] COMPRISE: 3-32,35-47,51-67,69-100: (A) RMSD REMARK 210 (ORDERED RESIDUES): BB, 0.6, HEAVY ATOM, 1.0. (B) RAMACHANDRAN REMARK 210 STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 90.6%, REMARK 210 ADDITIONALLY ALLOWED, 9.2%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, REMARK 210 0.1%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI- REMARK 210 PSI, -0.13/-0.20, ALL, -0.04/-0.24. (D) MOLPROBITY CLASH SCORE REMARK 210 (RAW/Z-): 20.04/-1.91 (E) RPF SCORES FOR GOODNESS OF FIT TO REMARK 210 NOESY DATA (RESIDUES 1-102): RECALL, 0.982, PRECISION, 0.910, F- REMARK 210 MEASURE, 0.945, DP-SCORE, 0.788. (F) NUMBER OF CLOSE CONTACTS REMARK 210 PER 20 MODELS: 16. (G) MOLPROBITY RAMACHANDRAN ANALYSIS (ALL REMARK 210 RESIDUES): THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN REMARK 210 (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND REMARK 210 HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE REMARK 210 FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < REMARK 210 1.8]: 1-2,33-34,48-50,68,101-102. 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 103 REMARK 465 HIS A 104 REMARK 465 HIS A 105 REMARK 465 HIS A 106 REMARK 465 HIS A 107 REMARK 465 HIS A 108 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 60 0.50 -69.91 REMARK 500 2 TYR A 35 30.13 -91.85 REMARK 500 2 GLU A 84 92.52 -68.92 REMARK 500 3 LYS A 17 89.61 -69.44 REMARK 500 3 ALA A 92 94.51 -67.65 REMARK 500 3 PRO A 100 35.21 -72.66 REMARK 500 4 LYS A 17 99.27 -67.30 REMARK 500 5 LYS A 17 95.69 -62.54 REMARK 500 5 TYR A 35 27.54 -74.91 REMARK 500 6 LYS A 17 95.39 -60.91 REMARK 500 6 PRO A 53 94.49 -68.89 REMARK 500 6 PHE A 55 1.00 -67.32 REMARK 500 6 LEU A 101 31.26 -88.65 REMARK 500 7 ILE A 58 -168.89 -118.38 REMARK 500 8 GLU A 84 92.03 -67.64 REMARK 500 9 GLU A 84 95.92 -68.17 REMARK 500 10 ASP A 2 128.07 -173.99 REMARK 500 10 TYR A 35 21.50 -141.89 REMARK 500 10 PRO A 53 95.36 -66.01 REMARK 500 10 ILE A 58 -169.31 -115.94 REMARK 500 10 GLU A 84 92.20 -67.62 REMARK 500 10 ALA A 92 94.65 -63.63 REMARK 500 11 GLN A 3 -30.03 68.80 REMARK 500 11 LEU A 101 -66.55 -131.47 REMARK 500 12 TYR A 32 58.09 -140.28 REMARK 500 12 PRO A 53 95.51 -65.13 REMARK 500 12 ALA A 92 92.83 -69.02 REMARK 500 13 ASN A 45 14.17 -150.62 REMARK 500 13 ILE A 58 -169.12 -123.27 REMARK 500 14 LYS A 17 85.88 -63.73 REMARK 500 14 TYR A 35 36.01 -79.01 REMARK 500 14 ILE A 58 -169.81 -109.82 REMARK 500 17 ILE A 58 -169.70 -125.18 REMARK 500 17 GLN A 99 87.70 -150.97 REMARK 500 18 LYS A 19 99.05 -65.56 REMARK 500 18 PRO A 33 30.99 -76.45 REMARK 500 18 PRO A 47 -165.92 -72.49 REMARK 500 18 LYS A 51 -47.91 74.57 REMARK 500 18 SER A 65 30.22 -88.11 REMARK 500 18 GLU A 84 91.95 -67.17 REMARK 500 19 TYR A 35 46.98 -79.01 REMARK 500 19 PHE A 55 1.88 -69.62 REMARK 500 19 SER A 60 4.48 -65.18 REMARK 500 20 TYR A 35 36.88 -83.52 REMARK 500 20 PRO A 53 94.61 -68.23 REMARK 500 20 ALA A 92 95.96 -62.62 REMARK 500 20 LEU A 101 23.20 -160.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KIF RELATED DB: PDB REMARK 900 RELATED ID: VPR247 RELATED DB: TARGETDB DBREF 2KIM A 1 100 UNP A6B4U8 A6B4U8_VIBPA 1 100 SEQADV 2KIM LEU A 101 UNP A6B4U8 EXPRESSION TAG SEQADV 2KIM GLU A 102 UNP A6B4U8 EXPRESSION TAG SEQADV 2KIM HIS A 103 UNP A6B4U8 EXPRESSION TAG SEQADV 2KIM HIS A 104 UNP A6B4U8 EXPRESSION TAG SEQADV 2KIM HIS A 105 UNP A6B4U8 EXPRESSION TAG SEQADV 2KIM HIS A 106 UNP A6B4U8 EXPRESSION TAG SEQADV 2KIM HIS A 107 UNP A6B4U8 EXPRESSION TAG SEQADV 2KIM HIS A 108 UNP A6B4U8 EXPRESSION TAG SEQRES 1 A 108 MET ASP GLN PHE LEU VAL GLN ILE PHE ALA VAL ILE HIS SEQRES 2 A 108 GLN ILE PRO LYS GLY LYS VAL SER THR TYR GLY GLU ILE SEQRES 3 A 108 ALA LYS MET ALA GLY TYR PRO GLY TYR ALA ARG HIS VAL SEQRES 4 A 108 GLY LYS ALA LEU GLY ASN LEU PRO GLU GLY SER LYS LEU SEQRES 5 A 108 PRO TRP PHE ARG VAL ILE ASN SER GLN GLY LYS ILE SER SEQRES 6 A 108 LEU LYS GLY ARG ASP LEU ASP ARG GLN LYS GLN LYS LEU SEQRES 7 A 108 GLU ALA GLU GLY ILE GLU VAL SER GLU ILE GLY LYS ILE SEQRES 8 A 108 ALA LEU ARG LYS TYR LYS TRP GLN PRO LEU GLU HIS HIS SEQRES 9 A 108 HIS HIS HIS HIS HELIX 1 1 ASP A 2 HIS A 13 1 12 HELIX 2 2 TYR A 23 GLY A 31 1 9 HELIX 3 3 TYR A 35 GLY A 44 1 10 HELIX 4 4 PRO A 53 PHE A 55 5 3 HELIX 5 5 GLY A 68 ALA A 80 1 13 HELIX 6 6 ALA A 92 LYS A 97 1 6 SHEET 1 A 2 SER A 21 THR A 22 0 SHEET 2 A 2 VAL A 57 ILE A 58 1 O ILE A 58 N SER A 21 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