+Open data
-Basic information
Entry | Database: PDB / ID: 7urp | ||||||
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Title | Second cohesin module from Sca5 of Ruminococcus bromii | ||||||
Components | Ribonucleases G and E | ||||||
Keywords | PROTEIN BINDING / Cohesin / amylosome | ||||||
Function / homology | cellulose catabolic process / Immunoglobulin-like fold / membrane / Ribonucleases G and E Function and homology information | ||||||
Biological species | Ruminococcus bromii L2-63 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.03 Å | ||||||
Authors | Cerqueira, F. / Koropatkin, N. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structures of cohesin modules from Sca5 of 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 | 7urp.cif.gz | 86.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7urp.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 7urp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7urp_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7urp_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7urp_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 7urp_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/7urp ftp://data.pdbj.org/pub/pdb/validation_reports/ur/7urp | HTTPS FTP |
-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
#1: Protein | Mass: 17045.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminococcus bromii L2-63 (bacteria) / Gene: RBL236_00045 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A2N0UYJ0 |
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#2: Chemical | ChemComp-EDO / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.06M CaCl2, 0.06M MgCl2, 0.1M imidazole, 0.1M MES pH = 6.5, 30% PEG 20K, 30% PEGMME 500 |
-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: 0.729 Å | |||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Sep 10, 2018 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.729 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.03→30.1 Å / Num. obs: 87298 / % possible obs: 98.6 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12 | |||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.03→30.07 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.979 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.023 / 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: 100.89 Å2 / Biso mean: 18.107 Å2 / Biso min: 10.15 Å2
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Refinement step | Cycle: final / Resolution: 1.03→30.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.03→1.057 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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