2KIF
Solution NMR structure of an O6-methylguanine DNA methyltransferase family protein from Vibrio parahaemolyticus. Northeast Structural Genomics Consortium target VpR247.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 5 mM Shigemi | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
2 | 2D 1H-13C HSQC | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 5 mM Shigemi | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
3 | 3D simultaneous CN NOESY | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 5 mM Shigemi | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
4 | 3D 1H-13C NOESY aromatic | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 5 mM Shigemi | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
5 | 3D HNCO | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
6 | 3D HN(CA)CO | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
7 | 3D HNCA | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
8 | 3D CBCA(CO)NH | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
9 | 3D HNCACB | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
10 | 3D HBHA(CO)NH | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
11 | 3D HCCH-COSY aliphatic | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
12 | 3D HCCH-TOCSY aliphatic | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
13 | 3D (H)CCH-TOCSY aliphatic | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
14 | 3D HNHA | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
15 | 3D HN(CO)CA | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
16 | 2D 1H-15N hetNOE | 0.94 mM [U-100% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
17 | 1D 1H-15N T1 and T2 | 0.92 mM [U-5% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
18 | 2D 1H-13C HSQC high res. (L/V methyl stereoassignment) | 0.92 mM [U-5% 13C; U-100% 15N] VpR247, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 1.7 mM microtube | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 2448 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS, 125 DIHEDRAL ANGLE CONSTRAINTS, AND 62 HYDROGEN BOND CONSTRAINTS (26.1 CONSTRAINTS PER RESIDUE, 7.9 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 102 BY PSVS 1.3). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19, AND USING NEUTRAL HISTIDINE TAUTOMERS (NE2H FORM) AT POSITIONS 13 AND 38. | TopSpin |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA FOR BACKBONE AND SIDE CHAIN ASSIGNMENTS WERE OBTAINED ON A 1.7-MM MICROCRYOPROBE AT 600 MHZ. ALL NOESY DATA WERE ACQUIRED AT 800 MHZ USING A 5-MM CROYOPROBE. BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOS. HYDROGEN BOND CONSTRAINTS WERE DETERMINED USING BOTH AUTOSTRUCTURE AND CYANA, AND WERE APPLIED ONLY IN THE FINAL REFINEMENT STAGE (CNS) OF THE STRUCTURE DETERMINATION. ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE CONSTRAINED IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED ON PROCHECK AND MOLPROBITY. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 97.6%, SIDE CHAIN, 98.3%, AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 102, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-32,35-47,50-100: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 0.8. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 91.5%, ADDITIONALLY ALLOWED, 8.5%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.13/-0.20, ALL, -0.02/-0.12. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 18.92/-1.72 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-102): RECALL, 0.974, PRECISION, 0.937, F-MEASURE, 0.955, DP-SCORE, 0.835. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 6. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 1,33-34,48-49,101-102. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | 2.1 | Bruker Biospin |
2 | data analysis | TopSpin | 2.1 | Bruker Biospin |
3 | processing | NMRPipe | 2.3 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
4 | data analysis | Sparky | 3.112 | Goddard |
5 | peak picking | Sparky | 3.112 | Goddard |
6 | chemical shift assignment | PINE | 1.0 | Bahrami, Markley, Assadi, and Eghbalnia |
7 | chemical shift assignment | AutoAssign | 2.4.0 | Zimmerman, Moseley, Kulikowski and Montelione |
8 | validation | AutoAssign | 2.4.0 | Zimmerman, Moseley, Kulikowski and Montelione |
9 | structure solution | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
10 | refinement | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
11 | rpf analysis | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
12 | structure quality analysis | PSVS | 1.3 | Bhattacharya and Montelione |
13 | structure quality analysis | MolProbity | 3.15 | Richardson |
14 | pdb coordinate analysis | PdbStat | 5.1 | Tejero and Montelione |