2KPW
NMR solution structure of Lamin-B1 protein from Homo sapiens: Northeast Structural Genomics Consortium MEGA target, HR5546A (439-549)
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN | 90% H2O/10% D2O | 20mM NH4OAc, 5mM CACL2, 200mM NACL | 4.5 | AMBIENT | 298 | |
| 2 | 2D 1H-13C HSQC | 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN | 90% H2O/10% D2O | |||||
| 3 | 3D HNCACB | 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN | 90% H2O/10% D2O | |||||
| 4 | 3D CBCA(CO)NH | 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN | 90% H2O/10% D2O | |||||
| 5 | 3D HBHA(CO)NH | 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN | 90% H2O/10% D2O | |||||
| 6 | 3D HNCO | 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN | 90% H2O/10% D2O | |||||
| 7 | 3D HNHA | 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN | 90% H2O/10% D2O | |||||
| 8 | 3D HCCH-TOCSY | 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN | 90% H2O/10% D2O | |||||
| 9 | 3D 1H-15N NOESY | 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN | 90% H2O/10% D2O | |||||
| 10 | 3D 1H-13C NOESY | 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN | 90% H2O/10% D2O | |||||
| 11 | 2D HNOE | 1.129 MM [U-100% 13C; U-100% 15N] LAMIN-B1 PROTEIN | 90% H2O/10% D2O | |||||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| 2 | Bruker | AVANCE | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | FINAL STRUCTURE QUALITY FACTORS DETERMINED USING PSVS SOFTWARE: ORDERED RESIDUES ARE DEFINED AS:15A-32A,34A-37A,42A-47A,53A-72A,75A-79A,85A-91A,101A-106A, 110A-116A.(A) RMSD(ORDERED RESIDUES):BACKBONE ATOMS: 0.7A; ALL ATOMS: 1.0A.(B) RAMACHANDRAN STATISTICS FOR ALL ORDERED RESIDUES: MOST FAVOURED REGIONS: 83.1% ADDITIONALLY ALLOWED REGIONS:16.9% (C) PROCHECK SCORES FOR ALL ORDERED RESIDUES (RAW/Z): PHI-PSI -0.76/-2.68, ALL: -0.42/-2.48 (D) MOLPROBITY CLASH SCORE (RAW/Z): 20.38/-1.97. (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA: RECALL:0.962 PRECISION: 0.919 F-MEASURE: 0.94 DP-SCORE 0.794. | CNS |
| NMR Ensemble Information | |
|---|---|
| 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 | |
|---|---|
| Details | THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE SPECTROSCOPY. DATA FOR THE BACKBONE ASSIGNMENTS WAS ACQUIRED USING GFT NMR EXPERIMENTS. AUTOMATED RESONANCE ASSIGNMENTS WERE MADE USING AUTOASSIGN AND PATTERN-PICKER ALGORITHMS DEVELOPED FOR AUTOMATED ASSIGNMENTS OF GFT DATA. SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATED NOESY ASSIGNMENTS WERE MADE USING AUTOSTRUCTURE AND STRUCTURE SOLUTION WAS DETERMINED USING CYANA-2.1. 100 STRUCTURES WERE CALCULATED AND 20 BEST CONFORMERS WERE THEN REFINED IN A SHELL OF WATER USING CNS. INITIAL DIHEDRAL ANGLE CONSTRIANTS WERE OBTAINED FROM TALOS. COMPLETENESS OF THE ASSIGNMENTS INCLUDING THE N-TERMINAL 6XHIS TAG WERE BACKBONE:99% SIDECHAIN: 96%. THE ASSIGNMENTS WERE VALIDATED USING AVS SOFTWARE. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | CNS | 2.0.6 | BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ |
| 2 | chemical shift assignment | AutoAssign | 2.1 | Zimmerman, Moseley, Kulikowski and Montelione |
| 3 | chemical shift assignment | AVS | Moseley and Montelione | |
| 4 | processing | NMRPipe | 2008 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
| 5 | peak picking | Sparky | 2.3 | Goddard |
| 6 | structure solution | AutoStructure | 2.2.1 | Huang, Tejero, Powers and Montelione |
| 7 | geometry optimization | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
| 8 | collection | TopSpin | 2.1 | Bruker Biospin |
| 9 | collection | VnmrJ | 2.1 | Varian |
| 10 | data analysis | Sparky | 2.3 | Goddard |
| 11 | structure calculation | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
