- PDB-4mdw: Crystal structure of a DUF1541 family protein (ydhK) from Bacillu... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4mdw
Title
Crystal structure of a DUF1541 family protein (ydhK) from Bacillus subtilis subsp. subtilis str. 168 at 2.00 A resolution
Components
Uncharacterized protein YdhK
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF07563 family / DUF1541 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Domain of unknown function DUF1541 / Domain of unknown function DUF1541 / Protein of unknown function (DUF1541) / SH3 type barrels. / Roll / Mainly Beta / Uncharacterized protein YdhK
Function and homology information
Biological species
Bacillus subtilis subsp. subtilis (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence details
1. THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...1. THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 41-205 OF THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.
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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: 1.9 Å3/Da / Density % sol: 35.4 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 5.0% polyethylene glycol 3000, 40.0% polyethylene glycol 400, 0.1M MES pH 6.0, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 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
0.91837
1
2
0.97926
1
3
0.97885
1
Reflection
Resolution: 2→27.692 Å / Num. obs: 9897 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.41 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.1
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
0.692
1.4
2382
1527
83.9
2.07-2.15
0.605
1.7
3097
1727
95.7
2.15-2.25
0.431
2.2
3375
1873
96.9
2.25-2.37
0.36
2.7
3169
1824
96
2.37-2.52
0.267
3.6
3206
1814
95.4
2.52-2.71
0.238
4.1
3152
1767
96.7
2.71-2.99
0.143
5.9
3172
1847
95.9
2.99-3.42
0.07
10.8
3301
1811
96.5
3.42-4.3
0.038
16.9
3145
1768
95.4
4.3
0.03
21.1
3242
1793
94.1
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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
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 2→27.692 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.9135 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM ...Details: 1. ZERO OCCUPANCY HYDROGENS WERE INCLUDED DURING REFINEMENT TO IMPROVE THE ANTI-BUMPING RESTRAINTS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. MAD PHASE RESTRAINTS WERE USED DURING REFINEMENT. 7. LYSINE 195 APPEARS TO HAVE BEEN PROTECTED FROM REDUCTIVE METHYLATION AND WAS MODELED AS LYSINE. ALL OTHER LYSINES HAVE BEEN MODELED AS MLY (N-DIMETHYL-LYSINE).
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