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Yorodumi- PDB-2j9w: Structural insight into the ESCRT-I-II link and its role in MVB t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j9w | ||||||
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Title | Structural insight into the ESCRT-I-II link and its role in MVB trafficking | ||||||
Components | VPS28-PROV PROTEIN | ||||||
Keywords | PROTEIN TRANSPORT / NZF FINGER / HIV BUDDING | ||||||
Function / homology | Function and homology information ESCRT I complex / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway Similarity search - Function | ||||||
Biological species | XENOPUS LAEVIS (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Gill, D.J. / Teo, H.L. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Emr, S.D. / Williams, R.L. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Structural Insight Into the Escrt-I/-II Link and its Role in Mvb Trafficking. Authors: Gill, D.J. / Teo, H. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Emr, S.D. / Williams, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j9w.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j9w.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 2j9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j9w_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 2j9w_full_validation.pdf.gz | 435.1 KB | Display | |
Data in XML | 2j9w_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 2j9w_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/2j9w ftp://data.pdbj.org/pub/pdb/validation_reports/j9/2j9w | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999673, 0.025394, -0.002661), Vector: |
-Components
#1: Protein | Mass: 12000.693 Da / Num. of mol.: 2 / Fragment: RESIDUES 123-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q7T0W4 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.2 % |
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Crystal grow | pH: 6.5 Details: 15-25% PEG 600, 0.15M POTASSIUM THIOCYANATE, 0.2M SODIUM CHLORIDE, 0.1M GUANIDINE HYDROCHLORIDE, 0.1M SODIUM CACODYLATE PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 12, 2006 / Details: TORODIAL MIRROR |
Radiation | Monochromator: KHOZU / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→44.86 Å / Num. obs: 8573 / % possible obs: 88.3 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.57 |
Reflection shell | Resolution: 2.2→2.23 Å / Redundancy: 1.17 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.28 / % possible all: 45.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SE DATASET FROM SEMET SUBSTITUTED CRYSTAL Resolution: 1.3→44.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.987 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→44.86 Å
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Refine LS restraints |
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