+Open data
-Basic information
Entry | Database: PDB / ID: 4fla | ||||||
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Title | Crystal structure of human RPRD1B, carboxy-terminal domain | ||||||
Components | Regulation of nuclear pre-mRNA domain-containing protein 1B | ||||||
Keywords | TRANSCRIPTION / Structural Genomics Consortium / SGC | ||||||
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 / SAD / Resolution: 2.2 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: Nat.Struct.Mol.Biol. / Year: 2014 Title: RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. Authors: Ni, Z. / Xu, C. / Guo, X. / Hunter, G.O. / Kuznetsova, O.V. / Tempel, W. / Marcon, E. / Zhong, G. / Guo, H. / Kuo, W.H. / Li, J. / Young, P. / Olsen, J.B. / Wan, C. / Loppnau, P. / El ...Authors: Ni, Z. / Xu, C. / Guo, X. / Hunter, G.O. / Kuznetsova, O.V. / Tempel, W. / Marcon, E. / Zhong, G. / Guo, H. / Kuo, W.H. / Li, J. / Young, P. / Olsen, J.B. / Wan, C. / Loppnau, P. / El Bakkouri, M. / Senisterra, G.A. / He, H. / Huang, H. / Sidhu, S.S. / Emili, A. / Murphy, S. / Mosley, A.L. / Arrowsmith, C.H. / 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 | 4fla.cif.gz | 209.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fla.ent.gz | 170.7 KB | Display | PDB format |
PDBx/mmJSON format | 4fla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/4fla ftp://data.pdbj.org/pub/pdb/validation_reports/fl/4fla | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17365.674 Da / Num. of mol.: 4 / Fragment: UNP residues 172-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPRD1B, C20orf77, CREPT / Plasmid: pET28 MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NQG5 #2: Chemical | ChemComp-UNX / #3: 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: 3.1 Å3/Da / Density % sol: 60.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 25% PEG-3350, 0.2M ammonium acetate, 0.1M HEPES, pH 7.5, vapor diffusion, temperature 291K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.2→47.63 Å / Num. obs: 37701 / % possible obs: 99.98 % / Redundancy: 9.62 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 15.5351 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.46 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. unmerged intensities (SCALEPACK) for a selenomethionine derivative are included with the deposited structure ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED. unmerged intensities (SCALEPACK) for a selenomethionine derivative are included with the deposited structure factors. Discontinuities and ambiguity of electron density defining residues 190 through 194 cause us to question the register of the amino acid sequence fitted N-terminal of that region. The programs resolve, arp/warp, dm were used in density improvement of the original Se-Met maps. Buccaneer was used for model tracing. COOT and the MOLPROBITY server were also used during refinement.
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.95 Å2 / Biso mean: 44.226 Å2 / Biso min: 13.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→40 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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