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Yorodumi- PDB-2xpp: Crystal structure of a Spt6-Iws1(Spn1) complex from Encephalitozo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xpp | ||||||
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Title | Crystal structure of a Spt6-Iws1(Spn1) complex from Encephalitozoon cuniculi, Form III | ||||||
Components |
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Keywords | TRANSCRIPTION / ELONGATION / HISTONE CHAPERONE / RNA POLYMERASE II / MRNA EXPORT | ||||||
Function / homology | Function and homology information nucleosome organization / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription elongation factor complex / histone binding / nucleus Similarity search - Function | ||||||
Biological species | ENCEPHALITOZOON CUNICULI (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Diebold, M.-L. / Koch, M. / Cura, V. / Cavarelli, J. / Romier, C. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: The Structure of an Iws1/Spt6 Complex Reveals an Interaction Domain Conserved in Tfiis, Elongin a and Med26 Authors: Diebold, M.-L. / Koch, M. / Loeliger, E. / Cura, V. / 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 | 2xpp.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xpp.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/2xpp ftp://data.pdbj.org/pub/pdb/validation_reports/xp/2xpp | HTTPS FTP |
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-Related structure data
Related structure data | 2xplSC 2xpnC 2xpoC C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 16424.105 Da / Num. of mol.: 1 / Fragment: EVOLUTIONARY CONSERVED DOMAIN, RESIDUES 55-198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENCEPHALITOZOON CUNICULI (fungus) / Plasmid: PNCS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SUS7 |
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#2: Protein/peptide | Mass: 4868.177 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT, RESIDUES 34-71 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENCEPHALITOZOON CUNICULI (fungus) / Plasmid: PNEA-TH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8SRG7 |
#3: Water | ChemComp-HOH / |
Sequence details | B 30-31 PART OF THROMBIN CLEAVAGE SITE. B 32-33 PART OF NDEI CLONING SITE. |
-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: 41.4 % / Description: NONE |
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Crystal grow | pH: 7 Details: 0.1 M SUCCINIC ACID/SODIUM DIHYDROGEN PHOSPHATE/GLYCINE SYSTEM PH 7.0 33% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.977 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 19, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→50 Å / Num. obs: 18952 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 44.6 |
Reflection shell | Resolution: 1.74→1.81 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 9.2 / % possible all: 99.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XPL Resolution: 1.74→58.22 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.166 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
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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: 24.464 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→58.22 Å
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Refine LS restraints |
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