- PDB-4dad: Crystal structure of a Putative pilus assembly-related protein (B... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4dad
Title
Crystal structure of a Putative pilus assembly-related protein (BPSS2195) from Burkholderia pseudomallei K96243 at 2.50 A resolution (PSI Community Target, Shapiro L.)
Components
Putative pilus assembly-related protein
Keywords
SIGNALING PROTEIN / SIGNAL TRANSDUCTION / Response regulator receiver domain / CheY-related protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG FOLLOWED BY RESIDUES 1-127 OF THE FULL LENGTH PROTEIN.
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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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.00M (NH4)2SO4, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2011 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
0.97947
1
2
0.91837
1
3
0.97894
1
Reflection
Resolution: 2.5→42.953 Å / Num. obs: 5865 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.77 % / Biso Wilson estimate: 61.811 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.22
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2.5-2.59
4.83
0.643
2.56
2700
559
97.4
2.59-2.69
0.472
3.4
2769
548
99.6
2.69-2.81
0.379
4.2
2958
587
99.2
2.81-2.96
0.241
6.4
2790
557
98.8
2.96-3.15
0.152
9.5
2891
614
99
3.15-3.39
0.092
15
2540
559
99.3
3.39-3.73
0.058
21.9
2988
596
99.5
3.73-4.26
0.042
28
2826
587
98.8
4.26-5.35
0.036
32.4
2592
591
98
5.35-42.953
0.032
34.8
2851
658
97.9
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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
December29, 2011
datascaling
BUSTER-TNT
2.10.0
refinement
XDS
datareduction
SHELXD
phasing
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 2.5→42.953 Å / Cor.coef. Fo:Fc: 0.9426 / Cor.coef. Fo:Fc free: 0.8994 / Occupancy max: 1 / Occupancy min: 0.5 / 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. SULFATE (SO4) FROM CRYSTALLIZATION CONDITION AND CHLORIDE (CL) FROM THE EXPRESSION OR PURIFICATION BUFFERS ARE MODELED INTO THE STRUCTURE 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
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