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Yorodumi- PDB-2xp1: Structure of the tandem SH2 domains from Antonospora locustae tra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xp1 | ||||||
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Title | Structure of the tandem SH2 domains from Antonospora locustae transcription elongation factor Spt6 | ||||||
Components | SPT6 | ||||||
Keywords | TRANSCRIPTION / IWS1 / HISTONE CHAPERONE / MRNA EXPORT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ANTONOSPORA LOCUSTAE (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å | ||||||
Authors | Diebold, M.-L. / Koch, M. / Cavarelli, J. / Romier, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Noncanonical Tandem Sh2 Enables Interaction of Elongation Factor Spt6 with RNA Polymerase II. Authors: Diebold, M. / Loeliger, E. / Koch, M. / Winston, F. / Cavarelli, J. / Romier, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xp1.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xp1.ent.gz | 67.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xp1_validation.pdf.gz | 435.4 KB | Display | wwPDB validaton report |
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Full document | 2xp1_full_validation.pdf.gz | 438.1 KB | Display | |
Data in XML | 2xp1_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 2xp1_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/2xp1 ftp://data.pdbj.org/pub/pdb/validation_reports/xp/2xp1 | 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: 20928.736 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 779-956 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANTONOSPORA LOCUSTAE (fungus) / Plasmid: PNEA-TH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E2QR95*PLUS | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Sequence details | UNPUBLISHED. GLY A779, SER A780 RESIDUE PROVIDED BY THE THROMBIN CLEAVAGE SITE. HIS A781, MET A782 ...UNPUBLISHE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.3 % / Description: NONE |
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Crystal grow | pH: 6 Details: 0.1 M MES PH 6.0, 1.5 M AMMONIUM SULFATE, 20 MM COCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 29, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→32 Å / Num. obs: 9257 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 47.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 52.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 7.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS Starting model: NONE Resolution: 2.2→32.07 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 21.802 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: 57.029 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→32.07 Å
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Refine LS restraints |
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