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Yorodumi- PDB-4l8j: Crystal structure of a Putative efflux transporter (BACEGG_01895)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4l8j | ||||||
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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 | ||||||
Biological species | Bacteroides eggerthii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.06 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a Putative efflux transporter (BACEGG_01895) from Bacteroides eggerthii DSM 20697 at 2.06 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l8j.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l8j.ent.gz | 115.4 KB | Display | PDB format |
PDBx/mmJSON format | 4l8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/4l8j ftp://data.pdbj.org/pub/pdb/validation_reports/l8/4l8j | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36749.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides eggerthii (bacteria) / Strain: DSM 20697 / Gene: BACEGG_01895, ZP_03459111.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7AHL2 | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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 PURIFICATI | |
-Experimental details
-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 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.83 Details: 12.0% polyethylene glycol 8000, 0.1M sodium chloride, 0.1M CAPS pH 9.83, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97871, 0.91837, 0.97817 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | 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 |
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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
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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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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Displacement parameters | Biso max: 116.81 Å2 / Biso mean: 46.9515 Å2 / Biso min: 24.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.339 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.06→46.486 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.06→2.13 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Origin x: 21.2691 Å / Origin y: 10.4219 Å / Origin z: 54.4325 Å
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Refinement TLS group | Selection details: { A|25 - 350 } |