- PDB-3hbk: Crystal structure of putative glycosyl hydrolase, was Domain of U... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3hbk
Title
Crystal structure of putative glycosyl hydrolase, was Domain of Unknown Function (DUF1080) (YP_001302580.1) from Parabacteroides distasonis ATCC 8503 at 2.36 A resolution
Components
putative glycosyl hydrolase
Keywords
HYDROLASE / YP_001302580.1 / putative glycosyl hydrolase / was Domain of Unknown Function (DUF1080) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function
Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Sequence details
SEQUENCE SEQUENCE THIS CONSTRUCT (RESIDUE 29-268) WAS EXPRESSED WITH A PURIFICATION TAG ...SEQUENCE SEQUENCE THIS CONSTRUCT (RESIDUE 29-268) 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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2000M Li2SO4, 30.0000% PEG-4000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 2.36→29.336 Å / Num. obs: 13756 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 60.809 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.77
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2.36-2.44
0.951
1.4
8328
2216
1
92.8
2.44-2.54
0.744
1.9
9886
2560
1
99.8
2.54-2.66
0.52
2.6
9995
2583
1
100
2.66-2.8
0.375
3.7
9560
2474
1
99.9
2.8-2.97
0.244
5.6
9363
2415
1
99.7
2.97-3.2
0.134
9.7
9680
2508
1
99.9
3.2-3.52
0.076
16.5
9598
2475
1
100
3.52-4.03
0.045
25.7
9680
2505
1
99.8
4.03-5.06
0.034
32.7
9667
2497
1
99.8
5.06-29.336
0.031
36.5
9779
2533
1
99.2
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.36→29.336 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 14.445 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.285 / ESU R Free: 0.226 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. SULFATE (SO4) AND ETHYLENE GLYCOL (EDO) HAVE BEEN MODELED FROM CRYSTALLIZATION/CRYO CONDITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.245
685
5 %
RANDOM
Rwork
0.198
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obs
0.2
13695
99.71 %
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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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