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Yorodumi- PDB-6idr: Crystal structure of Vibrio cholerae MATE transporter VcmN in the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6idr | ||||||
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Title | Crystal structure of Vibrio cholerae MATE transporter VcmN in the bent form | ||||||
Components | MATE family efflux transporter | ||||||
Keywords | TRANSPORT PROTEIN / MATE multidrug transporter | ||||||
Function / homology | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / : Function and homology information | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.502 Å | ||||||
Authors | Kusakizako, T. / Claxton, D.P. / Tanaka, Y. / Maturana, A.D. / Kuroda, T. / Ishitani, R. / Mchaourab, H.S. / Nureki, O. | ||||||
Citation | Journal: Structure / Year: 2019 Title: Structural Basis of H+-Dependent Conformational Change in a Bacterial MATE Transporter. Authors: Kusakizako, T. / Claxton, D.P. / Tanaka, Y. / Maturana, A.D. / Kuroda, T. / Ishitani, R. / Mchaourab, H.S. / Nureki, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6idr.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6idr.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 6idr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6idr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6idr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6idr_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6idr_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/6idr ftp://data.pdbj.org/pub/pdb/validation_reports/id/6idr | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47523.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CGT79_05080 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2A1YWE9 | ||
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#2: Chemical | ChemComp-OLC / ( #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.72 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / Details: PEG 300, sodium citrate, ammonium fluoride |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 15, 2013 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.5→93.74 Å / Num. obs: 17737 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 31.16 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.232 / Rpim(I) all: 0.096 / Rrim(I) all: 0.252 / Net I/σ(I): 5.9 / Num. measured all: 118705 / Scaling rejects: 816 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 2.502→50.121 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.71 Å2 / Biso mean: 34.9442 Å2 / Biso min: 12.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.502→50.121 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %
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