+Open data
-Basic information
Entry | Database: PDB / ID: 7uvg | ||||||
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Title | First cohesin of Sca5 from Ruminococcus bromii | ||||||
Components | Coh5 | ||||||
Keywords | PROTEIN BINDING / amylosome cohesin dockerin Ruminococcus bromii | ||||||
Function / homology | IODIDE ION Function and homology information | ||||||
Biological species | Ruminococcus bromii L2-63 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å | ||||||
Authors | Cerqueira, F. / Koropatkin, N. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structures of Sca5 cohesin modules from Ruminococcus bromii Authors: Cerqueira, F. / Koropatkin, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7uvg.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uvg.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 7uvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/7uvg ftp://data.pdbj.org/pub/pdb/validation_reports/uv/7uvg | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 20548.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus bromii L2-63 (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) | ||||
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#2: Chemical | ChemComp-EDO / | ||||
#3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M ZnCl2, 18% PEG 8000, 100mM Na cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å | ||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 6, 2020 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.77→22.04 Å / Num. obs: 17738 / % possible obs: 96.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.47 | ||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.77→22 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.069 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.55 Å2 / Biso mean: 38.235 Å2 / Biso min: 27.38 Å2
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Refinement step | Cycle: final / Resolution: 1.77→22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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