- PDB-4iyk: Crystal structure of a putative carbohydrate binding protein (BAC... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4iyk
Title
Crystal structure of a putative carbohydrate binding protein (BACUNI_04699) from Bacteroides uniformis ATCC 8492 at 2.00 A resolution
Components
Uncharacterized protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF12866 family protein / DUF3823 / putative carbohydrate binding protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information
DUF3823, N-terminal / Domain of unknown function DUF3823_C / Protein of unknown function (DUF3823) N-terminal domain / Domain of unknown function (DUF3823_C) / Immunoglobulin-like - #2060 / Carboxypeptidase-like, regulatory domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 241 / 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 15-238 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: 2.54 Å3/Da / Density % sol: 51.49 %
Resolution: 2→28.31 Å / Num. obs: 17020 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 31.372 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.22
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
2-2.07
0.44
2.2
7641
3040
1
92
2.07-2.15
0.335
3.2
9317
3178
1
98.5
2.15-2.25
0.241
4.3
9723
3326
1
98.5
2.25-2.37
0.184
5.7
9874
3382
1
98.4
2.37-2.52
0.132
7.8
9657
3302
1
98.9
2.52-2.71
0.098
10.6
9439
3232
1
98.6
2.71-2.99
0.061
16.6
9901
3401
1
98.9
2.99-3.42
0.035
26.9
9487
3277
1
98.7
3.42-4.3
0.027
34.4
9402
3286
1
99.2
4.3-28.31
0.022
39.1
9559
3334
1
98.5
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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
March15, 2012
datascaling
BUSTER-TNT
refinement
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 2→28.31 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.9331 / Occupancy max: 1 / Occupancy min: 0.15 / 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.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.CHLORIDE (CL) AND 1,2-ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTION ARE MODELED.
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