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Yorodumi- PDB-5jjt: Crystal structure of a type 5 serine/threonine protein phosphatas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jjt | ||||||
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Title | Crystal structure of a type 5 serine/threonine protein phosphatase from Arabidopsis thaliana | ||||||
Components | Serine/threonine-protein phosphatase 5 | ||||||
Keywords | HYDROLASE / phosphatase | ||||||
Function / homology | Function and homology information negative regulation of chlorophyll biosynthetic process / red or far-red light signaling pathway / chloroplast-nucleus signaling pathway / tetrapyrrole binding / plasmodesma / nucleocytoplasmic transport / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity ...negative regulation of chlorophyll biosynthetic process / red or far-red light signaling pathway / chloroplast-nucleus signaling pathway / tetrapyrrole binding / plasmodesma / nucleocytoplasmic transport / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / nuclear envelope / nuclear membrane / nuclear speck / endoplasmic reticulum membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å | ||||||
Authors | Li, H.M. / Pu, H. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of a type 5 serine/threonine protein phosphatase from Arabidopsis thaliana Authors: Li, H.M. / Pu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jjt.cif.gz | 216.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jjt.ent.gz | 168.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jjt_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 5jjt_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 5jjt_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 5jjt_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/5jjt ftp://data.pdbj.org/pub/pdb/validation_reports/jj/5jjt | HTTPS FTP |
-Related structure data
Related structure data | 1waoS 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: 54169.391 Da / Num. of mol.: 2 / Fragment: UNP residues 5-483 of isoform 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PAPP5, PP5, At2g42810, F7D19.19 / Production host: Escherichia coli (E. coli) References: UniProt: Q84XU2, protein-serine/threonine phosphatase #2: Chemical | ChemComp-NI / #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: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.1M HEPES pH7.2, 22.5% PEG 3350, 20% glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 55086 / % possible obs: 96.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.97 |
Reflection shell | Resolution: 2.1→2.18 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WAO Resolution: 2.103→45.797 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.62 Å2 / Biso mean: 18.8251 Å2 / Biso min: 4.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.103→45.797 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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