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Yorodumi- PDB-2xvc: Molecular and structural basis of ESCRT-III recruitment to membra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xvc | ||||||
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Title | Molecular and structural basis of ESCRT-III recruitment to membranes during archaeal cell division | ||||||
Components |
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Keywords | CELL CYCLE / CELL DIVISION / CYTOKINESIS / WINGED-HELIX | ||||||
Function / homology | Function and homology information CdvA-like coiled-coil domain / CdvA-like coiled-coil domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Samson, R.Y. / Obita, T. / Hodgson, B. / Shaw, M.K. / Chong, P.L. / Williams, R.L. / Bell, S.D. | ||||||
Citation | Journal: Mol.Cell / Year: 2011 Title: Molecular and Structural Basis of Escrt-III Recruitment to Membranes During Archaeal Cell Division. Authors: Samson, R.Y. / Obita, T. / Hodgson, B. / Shaw, M.K. / Chong, P.L. / Williams, R.L. / Bell, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xvc.cif.gz | 26.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xvc.ent.gz | 16.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xvc_validation.pdf.gz | 426.2 KB | Display | wwPDB validaton report |
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Full document | 2xvc_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | 2xvc_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 2xvc_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/2xvc ftp://data.pdbj.org/pub/pdb/validation_reports/xv/2xvc | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 6831.850 Da / Num. of mol.: 1 / Fragment: WINGED-HELIX DOMAIN, RESIDUES 210-259 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: TO149 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q97ZJ6 | ||
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#2: Protein/peptide | Mass: 1633.988 Da / Num. of mol.: 1 / Fragment: RESIDUES 251-265 / Source method: obtained synthetically / Source: (synth.) SULFOLOBUS SOLFATARICUS (archaea) / References: UniProt: Q97ZJ5 | ||
#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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | pH: 4 / Details: 15% PEG 4000, 5 MM CDCL2, PH 4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.54 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→60.99 Å / Num. obs: 8461 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 20.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 5.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.15→56.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.026 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.149 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.373 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→56.5 Å
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Refine LS restraints |
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