- PDB-4l8j: Crystal structure of a Putative efflux transporter (BACEGG_01895)... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4l8j
Title
Crystal structure of a Putative efflux transporter (BACEGG_01895) from Bacteroides eggerthii DSM 20697 at 2.06 A resolution
Components
Putative efflux transporter
Keywords
TRANSPORT PROTEIN / HlyD family secretion protein / PF00529 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information
conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Beta Barrel / Orthogonal Bundle ...conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE CONSTRUCT (RESIDUES 24-350) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 24-350) 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: 3.09 Å3/Da / Density % sol: 60.15 %
Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
Radiation
Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.97871
1
2
0.91837
1
3
0.97817
1
Reflection
Resolution: 2.06→46.486 Å / Num. obs: 29410 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.746 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.77
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
2.06-2.13
0.884
2.2
18362
2727
99.9
2.13-2.22
0.671
2.9
20096
3040
99.9
2.22-2.32
0.444
4.1
17630
2861
99.9
2.32-2.44
0.358
5.3
19081
2815
99.9
2.44-2.59
0.255
7.1
19311
2885
99.9
2.59-2.79
0.184
9.5
18537
2917
99.9
2.79-3.07
0.104
15.9
19232
2939
100
3.07-3.52
0.064
24.2
19664
3016
99.9
3.52-4.42
0.042
34.5
18857
2971
99.6
4.42
0.037
37.9
19142
3239
99.2
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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
July4, 2012
datascaling
BUSTER-TNT
2.10.0
refinement
XDS
datareduction
SHELXD
phasing
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 2.06→46.486 Å / Cor.coef. Fo:Fc: 0.9367 / Cor.coef. Fo:Fc free: 0.9229 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. PEG FRAGMENTS (PEG) FROM THE CRYSTALLIZATION AND GLYCEROL (GOL) USED ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. PEG FRAGMENTS (PEG) FROM THE CRYSTALLIZATION AND GLYCEROL (GOL) USED AS A CRYOPROTECTANT HAVE BEEN MODELED INTO THE STRUCTURE.3. THE REFINEMEMT WAS RESTRAINED AGAINST THE MAD PHASES.
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