- PDB-3kez: Crystal structure of Putative sugar binding protein (YP_001299726... -
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Basic information
Entry
Database: PDB / ID: 3kez
Title
Crystal structure of Putative sugar binding protein (YP_001299726.1) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution
Components
Putative sugar binding protein
Keywords
SUGAR BINDING PROTEIN / Putative sugar binding protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
CRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.
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Components
#1: Protein
Putativesugarbindingprotein / Putative outer membrane protein / probably involved in nutrient binding
Mass: 18.015 Da / Num. of mol.: 998 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT (RESIDUES 23-482) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 23-482) 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 0.2000M (NH4)2HPO4, 20.0000% PEG-3350, No Buffer pH 7.9, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97919 Å / Relative weight: 1
Reflection
Resolution: 1.9→29.748 Å / Num. obs: 75204 / % possible obs: 99.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 15.886 Å2 / Rmerge(I) obs: 0.152 / Rsym value: 0.152 / Net I/σ(I): 8.9
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.9-1.95
3.5
0.643
1
18118
5109
0.643
92.9
1.95-2
4.2
0.583
1.3
22489
5301
0.583
98.4
2-2.06
5
0.512
1.5
26086
5251
0.512
100
2.06-2.12
5
0.424
1.8
25394
5103
0.424
100
2.12-2.19
5
0.351
2.2
24603
4949
0.351
100
2.19-2.27
5
0.306
2.5
23890
4803
0.306
100
2.27-2.36
5
0.275
2.8
22956
4615
0.275
100
2.36-2.45
5
0.245
3.1
22190
4457
0.245
100
2.45-2.56
5
0.212
3.6
21276
4267
0.212
100
2.56-2.69
5
0.181
4.2
20573
4129
0.181
100
2.69-2.83
5
0.161
4.7
19476
3899
0.161
100
2.83-3
5
0.133
5.6
18430
3698
0.133
100
3-3.21
5
0.112
6.6
17408
3495
0.112
100
3.21-3.47
5
0.092
7.5
16179
3266
0.092
100
3.47-3.8
5
0.082
8.1
14939
3017
0.082
100
3.8-4.25
4.9
0.068
9.9
13512
2742
0.068
100
4.25-4.91
4.9
0.064
10.4
11918
2431
0.064
100
4.91-6.01
4.8
0.076
9.2
9986
2076
0.076
100
6.01-8.5
4.7
0.075
8.8
7788
1649
0.075
100
8.5-29.75
4.3
0.059
10.2
4054
947
0.059
97.9
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Phasing
Phasing
Method: SAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.5.0053
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
SCALA
3.2.5
datascaling
PDB_EXTRACT
3.006
dataextraction
MOSFLM
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.9→29.748 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 6.859 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.134 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.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. 4.PHOSPHATE (PO4) AND 1,2-ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5.THE ELECTRON DENSITY NEAR RESIDUE 346 IN BOTH CHAINS HAS BEEN TENTATIVELY MODELED AS ENDOGENOUS CALCIUM (CA). A SIMILAR CALCIUM BINDING SITE IS PRESENT IN ANOTHER SUSD PROTEIN STRUCTURE, PDB ID 3CK7. 6.RAMACHANDRAN OUTLIERS AT RESIDUES A63 AND B63 ARE SUPPORTED BY ELECTRON DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.204
3785
5 %
RANDOM
Rwork
0.152
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obs
0.155
75129
99.31 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
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