- PDB-4oju: Crystal structure of a leucine-rich repeat protein (BACCAP_00569)... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4oju
Title
Crystal structure of a leucine-rich repeat protein (BACCAP_00569) from Bacteroides capillosus ATCC 29799 at 2.00 A resolution
Components
hypothetical leucine rich repeat protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Leucine rich repeats / PF13306 family protein / putative protein binding / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-170 OF 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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M magnesium chloride, 30.00% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Monochromator: Double Crystal Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979169 Å / Relative weight: 1
Reflection
Resolution: 2→29.42 Å / Num. obs: 46541 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.239 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 15.19
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2-2.07
0.776
2.9
64261
8585
99.6
2.07-2.15
0.581
4
66071
8605
100
2.15-2.25
0.452
5.2
69360
9033
100
2.25-2.37
0.345
6.6
69149
8985
100
2.37-2.52
0.255
8.7
69088
8958
100
2.52-2.71
0.204
10.7
66659
8650
100
2.71-2.99
0.13
15.9
69866
9106
100
2.99-3.42
0.077
23.9
65870
8757
100
3.42-4.3
0.048
33.9
63845
8768
100
4.3
0.037
39.7
66927
8909
99.6
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
PDB_EXTRACT
3.1
dataextraction
SHELX
phasing
SHARP
phasing
XSCALE
March15, 2012
datascaling
BUSTER-TNT
2.10.0
refinement
XDS
datareduction
SHELXD
phasing
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: SAD / Resolution: 2→29.42 Å / Cor.coef. Fo:Fc: 0.9532 / Cor.coef. Fo:Fc free: 0.9478 / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. 1,2 ETHANEDIOL (EDO) AND MG-ION FROM THE CRYOPROTECTANT AND FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. SOME N- and C-TERMINAL RESIDUES ARE DISORDERED. 5. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 6. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
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