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Yorodumi- PDB-1eia: X-RAY CRYSTAL STRUCTURE OF EQUINE INFECTIOUS ANEMIA VIRUS (EIAV) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eia | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF EQUINE INFECTIOUS ANEMIA VIRUS (EIAV) CAPSID PROTEIN P26 | ||||||
Components | EIAV CAPSID PROTEIN P26 | ||||||
Keywords | VIRAL PROTEIN / VIRAL CAPSID / EIAV / HIV / LENTIVIRUS | ||||||
Function / homology | Function and homology information viral budding via host ESCRT complex / viral nucleocapsid / nucleic acid binding / structural constituent of virion / zinc ion binding Similarity search - Function | ||||||
Biological species | Equine infectious anemia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / TREAT MAD AS MIR / Resolution: 2.7 Å | ||||||
Authors | Jin, Z. / Jin, L. / Peterson, D.L. / Lawson, C.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Model for lentivirus capsid core assembly based on crystal dimers of EIAV p26. Authors: Jin, Z. / Jin, L. / Peterson, D.L. / Lawson, C.L. #1: Journal: Biochim.Biophys.Acta / Year: 1997 Title: Cloning, Expression, Purification, and Characterization of the Major Core Protein (P26) from Equine Infectious Anemia Virus Authors: Birkett, A.J. / Yelamos, B. / Rodriguez-Crespo, I. / Gavilanes, F. / Peterson, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eia.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eia.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 1eia.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eia_validation.pdf.gz | 426.8 KB | Display | wwPDB validaton report |
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Full document | 1eia_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 1eia_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 1eia_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/1eia ftp://data.pdbj.org/pub/pdb/validation_reports/ei/1eia | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23487.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equine infectious anemia virus / Genus: Lentivirus / Gene: GAG / Gene (production host): GAG / Production host: Escherichia coli (E. coli) / References: UniProt: P69732 |
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#2: 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: 4.9 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.72 |
Detector | Type: BRANDEIS / Detector: CCD / Date: Nov 17, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.72 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→48 Å / Num. obs: 13201 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 40 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 17 % / Mean I/σ(I) obs: 6 / Rsym value: 0.335 / % possible all: 94.6 |
Reflection | *PLUS Lowest resolution: 48 Å / Num. all: 13201 / Num. obs: 12292 |
Reflection shell | *PLUS % possible obs: 94.6 % / Rmerge(I) obs: 0.357 |
-Processing
Software |
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Refinement | Method to determine structure: TREAT MAD AS MIR / Resolution: 2.7→48 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 55 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 48 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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