+Open data
-Basic information
Entry | Database: PDB / ID: 4hfg | |||||||||
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Title | CID of human RPRD1B | |||||||||
Components | Regulation of nuclear pre-mRNA domain-containing protein 1B | |||||||||
Keywords | PROTEIN BINDING / Structural Genomics Consortium / SGC / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information regulation of cell cycle process / RNA polymerase II promoter clearance / mRNA 3'-end processing / transcription preinitiation complex / RNA polymerase II complex binding / RNA polymerase II C-terminal domain binding / RNA polymerase II transcribes snRNA genes / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / nucleoplasm ...regulation of cell cycle process / RNA polymerase II promoter clearance / mRNA 3'-end processing / transcription preinitiation complex / RNA polymerase II complex binding / RNA polymerase II C-terminal domain binding / RNA polymerase II transcribes snRNA genes / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | |||||||||
Authors | Ni, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Guo, X. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. ...Ni, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Guo, X. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Greenblatt, J.F. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: TO BE PUBLISHED Title: CID of human RPRD1B Authors: Ni, Z. / Xu, C. / Tempel, W. / El Bakkouri, M. / Loppnau, P. / Guo, X. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Greenblatt, J.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hfg.cif.gz | 118.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hfg.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 4hfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/4hfg ftp://data.pdbj.org/pub/pdb/validation_reports/hf/4hfg | HTTPS FTP |
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-Related structure data
Related structure data | 4fu3C 4flbS S: Starting model for refinement C: citing same article (ref.) |
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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: 15560.666 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPRD1B, C20orf77, CREPT / Plasmid: pET15 MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NQG5 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-UNX / #4: 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: 2.2 Å3/Da / Density % sol: 43.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 30% PEG550MME, 0.1M ammounium sulfate, 0.1M sodium cacodylate, pH 6.5, vapor diffusion, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0441 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0441 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→40 Å / Num. obs: 18559 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.103 / Χ2: 1.473 / Net I/σ(I): 7.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4FLB Resolution: 2→36.73 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.2407 / WRfactor Rwork: 0.1708 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8192 / SU B: 10.533 / SU ML: 0.15 / SU R Cruickshank DPI: 0.1928 / SU Rfree: 0.1882 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. RESOLVE, BUCCANEER, DM, ARP/WARP, COOT, CHAINSAW AND MOLPROBITY SERVER WERE ALSO USED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.61 Å2 / Biso mean: 37.0332 Å2 / Biso min: 17.88 Å2
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Refinement step | Cycle: LAST / Resolution: 2→36.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / 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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