2L1P
NMR solution structure of the N-terminal domain of DNA-binding protein SATB1 from Homo sapiens: Northeast Structural Genomics Target HR4435B(179-250)
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 | 1.08 mM [U-100% 13C; U-100% 15N] HR4435B | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 298 | |
2 | 2D 1H-13C HSQC | 1.08 mM [U-100% 13C; U-100% 15N] HR4435B | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 298 | |
3 | 3D CBCA(CO)NH | 1.08 mM [U-100% 13C; U-100% 15N] HR4435B | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 298 | |
4 | 3D HNCACB | 1.08 mM [U-100% 13C; U-100% 15N] HR4435B | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 298 | |
5 | 3D HBHA(CO)NH | 1.08 mM [U-100% 13C; U-100% 15N] HR4435B | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 298 | |
6 | 3D HNCO | 1.08 mM [U-100% 13C; U-100% 15N] HR4435B | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 298 | |
7 | 3D HCCH-TOCSY | 1.08 mM [U-100% 13C; U-100% 15N] HR4435B | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 298 | |
8 | 3D 1H-15N NOESY | 1.08 mM [U-100% 13C; U-100% 15N] HR4435B | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 298 | |
9 | 3D 1H-13C NOESY | 1.08 mM [U-100% 13C; U-100% 15N] HR4435B | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 298 | |
10 | 2D 1H-15N HSQC | 1.08 mM [U-100% 13C; U-100% 15N] HR4435B | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 298 | |
11 | 2D 1H-13C HSQC | 1.08 mM [U-100% 13C; U-100% 15N] HR4435B | 90% H2O/10% D2O | 5mM CaCl2, 100mM NaCl | 6.5 | 1 atm | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | The structure was determined using triple resonance NMR spectroscopy. Automated backbone assignments were made using Autoassign. Sidechain assignments were completed manually. Automated NOESY assignments were made using AutoStructure and structure solution was obtained using AutoStructure and CYANA-2.1. 150 structures were calculated and 20 best structures were refined in a shell of water using CNS. Initial dihedral angles were obtained using TALOS. The structure calculations were done including the N-terminal 6xHis tag. Resonance assignments were validated using AVS validation software. Final quality scores were determined using PSVS software. Ordered residues are defined as:11-13,18-54,62-77 . RMSD(ordered residuesall backbone aatoms 0.9A; All heavy atoms 1.4A; Ramachandran Statistics for all ordered residues: Most favoured 94.6%, additionally allowed region: 5.4%; Procheck scores for all ordered residues (Raw/Z) phi-psi 0.09/0.67; All dihedral angles 0.04/0.24; MolProbity clash score (Raw/Z) 13.00/-0.71. RPF scores for the goodness of fir of the structure to the NMR data: recall:0.933; Precision 0.918; F-measure 0.926 and final DP score: 0.768 | AutoAssign |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 150 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | Data acquisition on B600 was performed using 35 uL of 1.08mM sample and a 1.7mm microcryoprobe. |
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 | geometry optimization | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
5 | structure solution | 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 |