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Yorodumi- PDB-5hqj: Crystal structure of ABC transporter Solute Binding Protein B1G1H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hqj | |||||||||
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Title | Crystal structure of ABC transporter Solute Binding Protein B1G1H7 from Burkholderia graminis C4D1M, target EFI-511179, in complex with D-arabinose | |||||||||
Components | Periplasmic binding protein/LacI transcriptional regulator | |||||||||
Keywords | SOLUTE-BINDING PROTEIN / ABC TRANSPORTER SOLUTE BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Burkholderia graminis C4D1M (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å | |||||||||
Authors | Roth, Y. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | |||||||||
Citation | Journal: To be published Title: Crystal structure of ABC transporter Solute Binding Protein B1G1H7 from Burkholderia graminis C4D1M, target EFI-511179, in complex with D-arabinose Authors: Roth, Y. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hqj.cif.gz | 174.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hqj.ent.gz | 143.9 KB | Display | PDB format |
PDBx/mmJSON format | 5hqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hqj_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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Full document | 5hqj_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 5hqj_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 5hqj_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/5hqj ftp://data.pdbj.org/pub/pdb/validation_reports/hq/5hqj | HTTPS FTP |
-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
#1: Protein | Mass: 33733.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia graminis C4D1M (bacteria) / Strain: C4D1M / Gene: BgramDRAFT_3172 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1G1H7 |
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#2: Sugar | ChemComp-64K / |
#3: Chemical | ChemComp-CL / |
#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: 1.94 Å3/Da / Density % sol: 36.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein (10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Arabinose); Reservoir (MCSG2 B2)(0.2 M Potassium Acetate 20 %(w/v) PEG 3350); Cryoprotection (20% Ethylene Glycol, 80% Reservoir) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 20, 2015 / Details: MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→50 Å / Num. obs: 37889 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 12.81 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.022 / Rrim(I) all: 0.061 / Χ2: 0.892 / Net I/av σ(I): 27.917 / Net I/σ(I): 10.3 / Num. measured all: 282195 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.55→27.991 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.71 / 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: 331.42 Å2 / Biso mean: 32.4823 Å2 / Biso min: 4.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→27.991 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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