2KL6
Solution NMR structure of the CARDB domain of PF1109 from Pyrococcus furiosus. Northeast Structural Genomics Consortium target PfR193A
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 | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
2 | 2D 1H-13C HSQC | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
3 | 3D 1H-15N NOESY | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
4 | 3D 1H-13C NOESY aliphatic | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
5 | 3D 1H-13C NOESY aromatic | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
6 | 2D 1H-13C HSQC high resolution (L/V methyl stereoassignment) | 0.43 mM [U-5% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
7 | 3D HNCO | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
8 | 3D HN(CA)CO | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
9 | 3D HN(CO)CA | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
10 | 3D HNCA | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
11 | 3D CBCA(CO)NH | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
12 | 3D HNCACB | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
13 | 3D HBHA(CO)NH | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
14 | 3D HCCH-TOCSY | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
15 | 3D HCCH-COSY | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
16 | 3D CCH-TOCSY | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
17 | 3D HNHA | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
18 | 2D 1H-15N hetNOE | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 90% H2O/10% D2O | 0.2 | 6.5 | ambient | 298 | |
19 | 1D 15N T1 and T2 | 0.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS | 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 2722 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 166 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (26.7 CONSTRAINTS PER RESIDUE, 11.5 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 108 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. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 1 TO 108, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 2-107: (A) RMSD (ORDERED RESIDUES): BB, 0.4, HEAVY ATOM, 0.6. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 93.3%, ADDITIONALLY ALLOWED, 6.5%, GENEROUSLY ALLOWED, 0.2%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.42/-1.34, ALL, -0.27/-1.60. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 15.99/-1.22 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 1-108): RECALL, 0.963, PRECISION, 0.951, F-MEASURE, 0.957, DP-SCORE, 0.861. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 4. | 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 PREDOMINANTLY 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 PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 98.7%, SIDE CHAIN, 99.0%, AROMATICS, 98.8%, STEREOSPECIFIC METHYL, 88.5%, STEREOSPECIFIC SIDE CHAIN NH2: 100%. THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. |
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 | structure solution | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
8 | refinement | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
9 | rpf analysis | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
10 | structure quality analysis | PSVS | 1.3 | Bhattacharya and Montelione |
11 | structure quality analysis | MolProbity | 3.15 | Richardson |
12 | pdb coordinate analysis | PdbStat | 5.1 | Tejero and Montelione |
13 | dihedral angle constraints | TALOS | plus | Cornilescu, Delaglio and Bax |