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Yorodumi- PDB-3ef1: The Structure of Fcp1, an essential RNA polymerase II CTD phosphatase -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ef1 | ||||||
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Title | The Structure of Fcp1, an essential RNA polymerase II CTD phosphatase | ||||||
Components | RNA polymerase II subunit A C-terminal domain phosphatase | ||||||
Keywords | HYDROLASE / phosphatase / CTD / FCPH / BRCT / BeF3 / acylphosphate analog / Cobalt / Magnesium / Manganese / Metal-binding / Nucleus / Protein phosphatase | ||||||
Function / homology | Function and homology information Formation of the Early Elongation Complex / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerase II CTD heptapeptide repeat phosphatase activity / signaling / myosin phosphatase activity / protein-serine/threonine phosphatase / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Ghosh, A. / Lima, C.D. | ||||||
Citation | Journal: Mol.Cell / Year: 2008 Title: The structure of Fcp1, an essential RNA polymerase II CTD phosphatase. Authors: Ghosh, A. / Shuman, S. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ef1.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ef1.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 3ef1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ef1_validation.pdf.gz | 434.7 KB | Display | wwPDB validaton report |
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Full document | 3ef1_full_validation.pdf.gz | 444.6 KB | Display | |
Data in XML | 3ef1_validation.xml.gz | 18 KB | Display | |
Data in CIF | 3ef1_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/3ef1 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/3ef1 | HTTPS FTP |
-Related 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: 50359.805 Da / Num. of mol.: 1 Fragment: FCP1 homology domain, Catalytically active fragment, UNP residues 140-580 Source method: isolated from a genetically manipulated source Details: leaves behind N-terminal S Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: fcp1, SPAC19B12.05c / Plasmid: pET28b-Smt3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus References: UniProt: Q9P376, protein-serine/threonine phosphatase |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Fcp1-BeF3-Mg was obtained by incubating 200 M Fcp1(140-580) with 225 M CTD peptide (SPSYSPTSPS), 300 M BeCl2, 5 mM NaF and 5 mM MgCl2 on ice for 1 h then crystallized by sitting drop vapor ...Details: Fcp1-BeF3-Mg was obtained by incubating 200 M Fcp1(140-580) with 225 M CTD peptide (SPSYSPTSPS), 300 M BeCl2, 5 mM NaF and 5 mM MgCl2 on ice for 1 h then crystallized by sitting drop vapor diffusion against 22% PEG-4000, 100 mM Na-citrate (pH 5.6), 100 mM ammonium acetate, 5% hexane 1,6-diol, 5% aminocaproic acid, 5% propane-1,3-diol, 5 mM DTT., VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 29320 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.059 / Χ2: 0.908 / Net I/σ(I): 19.043 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2784 / Χ2: 0.318 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→30 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.855 / Data cutoff high absF: 1787288 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.108 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.42 Å2 / Biso mean: 50.293 Å2 / Biso min: 23.05 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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