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Yorodumi- PDB-4ygy: Crystal Structure of Human Scp1 bound to trans-proline peptidomim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ygy | ||||||
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Title | Crystal Structure of Human Scp1 bound to trans-proline peptidomimetic CTD phospho-Ser5 peptide | ||||||
Components |
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Keywords | HYDROLASE / Phosphatase / Peptidomimetic / Complex | ||||||
Function / homology | Function and homology information RNA polymerase II CTD heptapeptide repeat phosphatase activity / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / protein-serine/threonine phosphatase / negative regulation of neuron differentiation / protein dephosphorylation / negative regulation of protein phosphorylation / negative regulation of neurogenesis / regulation of transcription by RNA polymerase II / extracellular exosome ...RNA polymerase II CTD heptapeptide repeat phosphatase activity / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / protein-serine/threonine phosphatase / negative regulation of neuron differentiation / protein dephosphorylation / negative regulation of protein phosphorylation / negative regulation of neurogenesis / regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.36 Å | ||||||
Authors | Mayfield, J.E. / Zhang, Y. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: Chemical Tools To Decipher Regulation of Phosphatases by Proline Isomerization on Eukaryotic RNA Polymerase II. Authors: Mayfield, J.E. / Fan, S. / Wei, S. / Zhang, M. / Li, B. / Ellington, A.D. / Etzkorn, F.A. / Zhang, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ygy.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ygy.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ygy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ygy_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 4ygy_full_validation.pdf.gz | 453.8 KB | Display | |
Data in XML | 4ygy_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 4ygy_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/4ygy ftp://data.pdbj.org/pub/pdb/validation_reports/yg/4ygy | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 21573.492 Da / Num. of mol.: 2 / Fragment: unp residues 76-254 / Mutation: D96N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTDSP1, NIF3, NLIIF, SCP1 / Production host: Escherichia coli (E. coli) References: UniProt: Q9GZU7, protein-serine/threonine phosphatase #2: Protein/peptide | Mass: 1259.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #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: 3.38 Å3/Da / Density % sol: 63.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 30% PEG 3350, 0.2 M magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03334 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03334 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.36→64.86 Å / Num. obs: 22534 / % possible obs: 96.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Χ2: 1.354 / Net I/av σ(I): 29.256 / Net I/σ(I): 15.3 / Num. measured all: 84442 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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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 / Resolution: 2.36→64.86 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.926 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 117.16 Å2 / Biso mean: 47.118 Å2 / Biso min: 27.24 Å2
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Refinement step | Cycle: final / Resolution: 2.36→64.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.359→2.421 Å / Total num. of bins used: 20
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