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Yorodumi- PDB-6lu2: Crystal structure of a substrate binding protein from Microbacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lu2 | ||||||
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Title | Crystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans | ||||||
Components | Substrate binding protein | ||||||
Keywords | TRANSPORT PROTEIN / Complex | ||||||
Biological species | Microbacterium hydrocarbonoxydans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||
Authors | Shimamura, K. / Akiyama, T. / Yokoyama, K. / Takenoya, M. / Ito, S. / Sasaki, Y. / Yajima, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Structural basis of substrate recognition by the substrate binding protein (SBP) of a hydrazide transporter, obtained from Microbacterium hydrocarbonoxydans. Authors: Shimamura, K. / Akiyama, T. / Yokoyama, K. / Takenoya, M. / Ito, S. / Sasaki, Y. / Yajima, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lu2.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lu2.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lu2_validation.pdf.gz | 423.9 KB | Display | wwPDB validaton report |
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Full document | 6lu2_full_validation.pdf.gz | 426.7 KB | Display | |
Data in XML | 6lu2_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 6lu2_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/6lu2 ftp://data.pdbj.org/pub/pdb/validation_reports/lu/6lu2 | 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: 53867.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microbacterium hydrocarbonoxydans (bacteria) Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
Sequence details | AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS GAT74979 FOR THE PROTEIN. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium acetate 0.1 M sodium cacodylate, pH 7.5 30% (w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9785 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 48691 / % possible obs: 99.3 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 50.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2301 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.75→39.551 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.107 Details: Hydrogens have been added in their riding positions SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.381 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→39.551 Å
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Refine LS restraints |
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LS refinement shell |
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