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Yorodumi- PDB-4rwe: The crystal structure of a sugar-binding transport protein from Y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rwe | ||||||
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Title | The crystal structure of a sugar-binding transport protein from Yersinia pestis CO92 | ||||||
Components | Sugar-binding transport protein | ||||||
Keywords | SUGAR BINDING PROTEIN / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å | ||||||
Authors | Tan, K. / Zhou, M. / Clancy, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a sugar-binding transport protein from Yersinia pestis CO92 Authors: Tan, K. / Zhou, M. / Clancy, S. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rwe.cif.gz | 126.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rwe.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 4rwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/4rwe ftp://data.pdbj.org/pub/pdb/validation_reports/rw/4rwe | 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: 30846.275 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: A1122_06015, Yersinia pestis / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: G0J922, UniProt: A0A2U2GYC0*PLUS | ||
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#2: Chemical | ChemComp-GOL / | ||
#3: Chemical | #4: 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: 2.47 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8M Ammonium citrate tribasic, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2014 / Details: Mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→34.66 Å / Num. all: 37067 / Num. obs: 37067 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 4.1 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1657 / % possible all: 89.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→34.66 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 26.17 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→34.66 Å
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Refine LS restraints |
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LS refinement shell |
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