- PDB-4ole: Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo ... -
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Basic information
Entry
Database: PDB / ID: 4ole
Title
Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution
Components
Next to BRCA1 gene 1 protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Ig-like domain from next to BRCA1 gene / PF16158 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information
regulation of bone mineralization / M band / phagophore assembly site / mitogen-activated protein kinase binding / peroxisomal membrane / regulation of stress-activated MAPK cascade / autophagosome / negative regulation of osteoblast differentiation / Pexophagy / ubiquitin binding ...regulation of bone mineralization / M band / phagophore assembly site / mitogen-activated protein kinase binding / peroxisomal membrane / regulation of stress-activated MAPK cascade / autophagosome / negative regulation of osteoblast differentiation / Pexophagy / ubiquitin binding / macroautophagy / mitochondrial intermembrane space / late endosome / receptor complex / lysosome / nuclear body / intracellular membrane-bounded organelle / zinc ion binding / nucleoplasm / membrane / cytosol Similarity search - Function
NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type ...NBR1, PB1 domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT (365-485) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (365-485) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 6.5 Å3/Da / Density % sol: 81.08 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.33 Details: 2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.97891
1
2
0.97949
1
3
0.91837
1
Reflection
Resolution: 2.52→48.72 Å / Num. obs: 50067 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.76 % / Biso Wilson estimate: 61.165 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 15.26
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.52-2.61
9.01
1.222
2.09
44101
4894
99.9
2.61-2.71
0.86
2.9
41822
4723
100
2.71-2.84
0.595
3.9
42578
5188
100
2.84-2.99
0.404
5.9
45565
4942
99.9
2.99-3.17
0.266
8.5
43534
4778
100
3.17-3.42
0.15
13.8
45707
5072
100
3.42-3.76
0.093
19.6
41139
4950
100
3.76-4.3
0.064
27.8
46279
5029
100
4.3-5.4
0.056
31.2
43207
5056
99.8
5.4-48.72
0.056
34
44593
5435
99.3
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
XSCALE
datascaling
BUSTER-TNT
2.10.0
refinement
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 2.52→48.72 Å / Cor.coef. Fo:Fc: 0.9329 / Cor.coef. Fo:Fc free: 0.9389 / Occupancy max: 1 / Occupancy min: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. SULFATE (SO4) AND ETHYLENE GLYCOL (EDO) MODELED WERE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
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