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Yorodumi- PDB-3u1u: Crystal structure of RNA polymerase-associated protein RTF1 homol... -
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-Basic information
Entry | Database: PDB / ID: 3u1u | ||||||
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Title | Crystal structure of RNA polymerase-associated protein RTF1 homolog Plus-3 domain | ||||||
Components | RNA polymerase-associated protein RTF1 homolog | ||||||
Keywords | TRANSCRIPTION / PLUS-3 / transcription elongation / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information blastocyst growth / Cdc73/Paf1 complex / endodermal cell fate commitment / stem cell population maintenance / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / Wnt signaling pathway / chromatin organization ...blastocyst growth / Cdc73/Paf1 complex / endodermal cell fate commitment / stem cell population maintenance / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / Wnt signaling pathway / chromatin organization / E3 ubiquitin ligases ubiquitinate target proteins / single-stranded DNA binding / nucleolus / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.8 Å | ||||||
Authors | Guo, Y. / Tempel, W. / Bian, C. / Wernimont, A.K. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Crystal structure of RNA polymerase-associated protein RTF1 homolog Plus-3 domain Authors: Guo, Y. / Tempel, W. / Bian, C. / Wernimont, A.K. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u1u.cif.gz | 122.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u1u.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 3u1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u1u_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
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Full document | 3u1u_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 3u1u_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 3u1u_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/3u1u ftp://data.pdbj.org/pub/pdb/validation_reports/u1/3u1u | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15917.687 Da / Num. of mol.: 2 / Fragment: unp residues 347-482 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RTF1, KIAA0252 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q92541 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-UNX / #5: 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: 2.7 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 291 K / Method: sitting drop vapor diffusion / pH: 5.5 Details: 25% PEG-3350, 0.2M ammonium sulfate, 0.1M sodium cacodylate, pH 5.5, sitting drop vapor diffusion, temperature 291K |
-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: Rigaku FR-E / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 17, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→30 Å / Num. all: 29993 / Num. obs: 29882 / % possible obs: 99.86 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.0335 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→28.54 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.951 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. The second data set attached is based on the same diffraction images as the refinement amplitudes but was ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. The second data set attached is based on the same diffraction images as the refinement amplitudes but was processed in HKL3000 and used for SAD phasing.
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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 max: 70.12 Å2 / Biso mean: 27.0878 Å2 / Biso min: 12.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→28.54 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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