- PDB-4fmr: Crystal structure of a Putative bacterial DNA binding protein (BV... -
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Open data
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Basic information
Entry
Database: PDB / ID: 4fmr
Title
Crystal structure of a Putative bacterial DNA binding protein (BVU_2165) from Bacteroides vulgatus ATCC 8482 at 2.25 A resolution
Components
uncharacterized hypothetical protein
Keywords
Structural Genomics / Unknown Function / Bacterial DNA binding protein / DUF4469 with IG-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
A: uncharacterized hypothetical protein B: uncharacterized hypothetical protein C: uncharacterized hypothetical protein D: uncharacterized hypothetical protein
Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT (RESIDUES 2-265) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 2-265) 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 20.0% 1,3-butanediol, 0.1M sodium acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9794 Å / Relative weight: 1
Reflection
Resolution: 2.25→29.682 Å / Num. obs: 52331 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 48.088 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.05
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
2.25-2.33
0.889
1.4
32721
9950
94.7
2.33-2.42
0.557
2.5
36732
10044
98.5
2.42-2.53
0.425
3.2
37836
10395
98.4
2.53-2.67
0.314
4.3
38927
11001
98.5
2.67-2.83
0.221
5.9
32930
9680
95.4
2.83-3.05
0.144
9
38501
10503
98.5
3.05-3.36
0.085
13.9
38371
10545
98.2
3.36-3.84
0.062
17.1
35186
10086
97.1
3.84-4.83
0.042
25.2
38659
10529
99
4.83
0.038
27.3
36782
10311
96.2
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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
December29, 2011
datascaling
BUSTER-TNT
2.10.0
refinement
XDS
datareduction
SHELXD
phasing
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: SAD / Resolution: 2.25→29.682 Å / Cor.coef. Fo:Fc: 0.9555 / Cor.coef. Fo:Fc free: 0.9311 / Occupancy max: 1 / Occupancy min: 0.22 / 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. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 6. THE REGION CONTAINING AN RAMACHRANDRAN OUTLIER (C221) HAS POOR DENSITY.
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