2K5Q
NMR Solution structure of membrane associated protein from Bacillus cereus: Northeast Structural Genomics Consortium Target: BcR97A
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 | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
2 | 2D 1H-13C HSQC | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
3 | 3D HNCO | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
4 | 3D CBCA(CO)NH | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
5 | 3D HNCACB | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
6 | 3D HBHA(CO)NH | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
7 | 3D C(CO)NH | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
8 | 3D HCCH-TOCSY | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
9 | 3D HCCH-COSY | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
10 | 3D 13C-edited_NOESY | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
11 | 3D 1H-15N NOESY | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
12 | 3D 13C-edited_NOESY | 1.25 mM [U-100% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
13 | 2D 1H-15N HSQC | 0.77 mM [U-10% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 | |
14 | 2D 1H-13C HSQC | 0.77 mM [U-10% 13C; U-100% 15N] BcR97A protein | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 293 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | The structure was determined using triple resonance NMR spectroscopy. Automated backbone resonance assignments were made using AutoAssign and pattern picker algorithms developed for automated assignments of GFT NMR data. Side chain assignments were completed manually. Automated NOESY assignments were made using AUTOSTRUCTURE and structure solution was determined using AUTOSTRUCTURE and CYANA-2.1. 176 structures were calculated and 20 best conformers were then refined in a shell of water using CNS. Initial Dihedral constriants were obtained from TALOS. The structure calculations were done including the C-terminal tag LEHHHHHH. Completeness of assignments excluding the 8-residue tag are: Backbone ~98.5%, sidechain ~ 95%, stereospecific methyl assignments 100%. The assignments were validated using the AVS software. Final structure quality factors determined using PSVS software: Ordered residues are defined as: 10-22,32-42,47-58,63-69,76-93. (a) RMSD(ordered residues) all Backbone atoms 0.9A; all heavy atoms 1.4A. (b) Ramachandran statistics for all ordered residues: Most favoured regions:85.9%, Additionally allowed regions 14.0%, Generously allowed region:0.2%. (c) Procheck scores for ordered residues (Raw/Z)phi-psi -0.73/-2.56, All:-0.49/-2.90 (d) MolProbity clash score (Raw/Z): 17.11/-1.41. (e) RPFscores for goodness of fit to NOESY data : Recall:0.963 Precision: 0.805F-measure:0.877 DP-score: 0.848 | AutoAssign |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 176 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | GFT (4,3)D data was acquired for backbone assignments. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | chemical shift assignment | AutoAssign | 2.2.1 | Zimmerman, Moseley, Kulikowski and Montelione |
2 | chemical shift assignment | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
3 | structure solution | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
4 | structure solution | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
5 | geometry optimization | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
6 | refinement | CNS | 2.0.6 | Brunger, Adams, Clore, Gros, Nilges and Read |
7 | geometry optimization | CNS | 2.0.6 | Brunger, Adams, Clore, Gros, Nilges and Read |