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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.