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Yorodumi- PDB-3l0b: Crystal structure of SCP1 phosphatase D206A mutant phosphoryl-int... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l0b | ||||||
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Title | Crystal structure of SCP1 phosphatase D206A mutant phosphoryl-intermediate | ||||||
Components | Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 | ||||||
Keywords | HYDROLASE / HAD superfamily / phosphoryl-aspartate intermediate / small C-terminal domain phosphatase / protein phosphatase | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Zhang, M. / Zhang, Y. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: Structural and functional analysis of the phosphoryl transfer reaction mediated by the human small C-terminal domain phosphatase, Scp1. Authors: Zhang, M. / Liu, J. / Kim, Y. / Dixon, J.E. / Pfaff, S.L. / Gill, G.N. / Noel, J.P. / Zhang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l0b.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l0b.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 3l0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l0b_validation.pdf.gz | 677 KB | Display | wwPDB validaton report |
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Full document | 3l0b_full_validation.pdf.gz | 684.4 KB | Display | |
Data in XML | 3l0b_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 3l0b_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/3l0b ftp://data.pdbj.org/pub/pdb/validation_reports/l0/3l0b | HTTPS FTP |
-Related structure data
Related structure data | 3l0cC 3l0yC 2ghqS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 21114.893 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN / Mutation: D206A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTDSP1, NIF3, NLIIF, SCP1 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9GZU7, protein-serine/threonine phosphatase #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-1PG / | #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: 3.34 Å3/Da / Density % sol: 63.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.5M AMMONIUM SULFATE, 0.2M LITHIUM SULFATE, 100MM HEPES, PH 7.0. CRYSTAL TRANSFERRED TO 100MM SODIUM CITRATE, PH 5.5, 30% PEG8000, 20MM PNPP, and 10mM Magnesium chloride, VAPOR DIFFUSION, ...Details: 0.5M AMMONIUM SULFATE, 0.2M LITHIUM SULFATE, 100MM HEPES, PH 7.0. CRYSTAL TRANSFERRED TO 100MM SODIUM CITRATE, PH 5.5, 30% PEG8000, 20MM PNPP, and 10mM Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2006 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→64.7 Å / Num. obs: 21278 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.071 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.204 / % possible all: 59.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2GHQ Resolution: 2.35→64.68 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 6.685 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 29.431 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→64.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.407 Å / Total num. of bins used: 20
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