- PDB-4dwe: Crystal structure of a putative polysaccharide deacetylase (BACOV... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4dwe
Title
Crystal structure of a putative polysaccharide deacetylase (BACOVA_03992) from Bacteroides ovatus ATCC 8483 at 2.01 A resolution
Components
uncharacterized protein
Keywords
Structural Genomics / Unknown Function / Hypothetical protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / CSAP
Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 21-499 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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.17M sodium acetate, 25.5% polyethylene glycol 4000, 15.0% Glycerol, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2012 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Radiation
Monochromator: double 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
0.9796
1
3
0.97925
1
Reflection
Resolution: 2.01→29.571 Å / Num. obs: 32317 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.32 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.17
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
2.01-2.08
0.437
1.8
10567
5721
95.2
2.08-2.17
0.344
2.3
13280
6571
98.1
2.17-2.26
0.271
2.8
11064
5494
97.9
2.26-2.38
0.236
3.3
12311
6103
97.2
2.38-2.53
0.203
3.8
12030
6050
97.3
2.53-2.73
0.154
4.9
11549
6064
95.6
2.73-3
0.111
6.8
12322
5962
98.1
3-3.43
0.07
10.6
12257
6003
97.7
3.43-4.32
0.042
16.2
11656
5962
95.8
4.32
0.037
19
12272
6028
96.6
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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
REFMAC
5.6.0117
refinement
XDS
datareduction
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.01→29.571 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.127 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.148 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS 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. GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1936
1596
4.9 %
RANDOM
Rwork
0.1486
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obs
0.1509
32268
98.78 %
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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: BABINET MODEL WITH MASK
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