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Yorodumi- PDB-5k23: Crystal structure of the complex between human phosphatase PRL-2 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k23 | ||||||
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Title | Crystal structure of the complex between human phosphatase PRL-2 in the oxidized state with the Bateman domain of human magnesium transporter CNNM3 | ||||||
Components |
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Keywords | HYDROLASE/TRANSPORTER PROTEIN/PROTEIN BINDING / Complex / phosphatase / magnesium transporter / protein binding / HYDROLASE / HYDROLASE-TRANSPORTER PROTEIN-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information prenylated protein tyrosine phosphatase activity / magnesium ion homeostasis / RAB geranylgeranylation / transmembrane transporter activity / monoatomic ion transport / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / early endosome / membrane ...prenylated protein tyrosine phosphatase activity / magnesium ion homeostasis / RAB geranylgeranylation / transmembrane transporter activity / monoatomic ion transport / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / early endosome / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96 Å | ||||||
Authors | Gulerez, I. / Kozlov, G. / Gehring, K. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: PRL3 phosphatase active site is required for binding the putative magnesium transporter CNNM3. Authors: Zhang, H. / Kozlov, G. / Li, X. / Wu, H. / Gulerez, I. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k23.cif.gz | 76.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k23.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 5k23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/5k23 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/5k23 | HTTPS FTP |
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-Related structure data
Related structure data | 5k24C 5k25C 5tsrC 1zckS 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: 21856.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTP4A2, PRL2, PTPCAAX2, BM-008 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q12974, protein-tyrosine-phosphatase |
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#2: Protein | Mass: 17634.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CNNM3, ACDP3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8NE01 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.54M sodium citrate, 0.1M sodium acetate, 10mM yttrium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9759 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 9, 2012 |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9759 Å / Relative weight: 1 |
Reflection | Resolution: 2.96→50 Å / Num. obs: 10491 / % possible obs: 99.51 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.047 / Net I/σ(I): 33.2 |
Reflection shell | Resolution: 2.96→3.04 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3.3 / % possible all: 94.06 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZCK Resolution: 2.96→49.02 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.909 / SU B: 17.731 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R: 1.023 / ESU R Free: 0.38 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.237 Å2
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Refinement step | Cycle: 1 / Resolution: 2.96→49.02 Å
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Refine LS restraints |
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