- PDB-4i17: Crystal structure of a TPR repeats protein (BF2334) from Bacteroi... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4i17
Title
Crystal structure of a TPR repeats protein (BF2334) from Bacteroides fragilis NCTC 9343 at 1.50 A resolution
Components
hypothetical protein
Keywords
Structural Genomics / Unknown Function / TPR repeats protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 19-245 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.43 Details: 2.6M ammonium sulfate, 0.1M MES pH 5.43, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution: 1.5→27.153 Å / Num. obs: 33966 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.734 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.65
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
1.5-1.55
0.841
2
22103
5487
85.6
1.55-1.62
0.672
2.6
31689
7577
98.8
1.62-1.69
0.512
3.3
27131
6418
98.3
1.69-1.78
0.362
4.6
28546
6717
98.2
1.78-1.89
0.24
6.7
28252
6565
97.5
1.89-2.04
0.134
11.1
29320
6791
96.7
2.04-2.24
0.078
17.1
27454
6336
95.7
2.24-2.56
0.057
22.3
27943
6411
94.4
2.56-3.23
0.041
29.4
27662
6349
92.1
3.23
0.029
39.9
28573
6077
88.3
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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
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 1.83→27.153 Å / Cor.coef. Fo:Fc: 0.9592 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 Details: OTHER REFINEMENT REMARKS: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR ...Details: OTHER REFINEMENT REMARKS: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ETHYLENE GLYCOL (GOL) FROM THE CRYOPROTECTANT AND AMMONIUM SULPHATE IONS FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4. TWO N-TERMINAL AND ONE C-TERMINAL RESIDUES ARE DISORDERED. 5. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
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