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Yorodumi- PDB-5zkk: Crystal structure of Phosphoserine phosphatase from Entamoeba his... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zkk | ||||||
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Title | Crystal structure of Phosphoserine phosphatase from Entamoeba histolytica | ||||||
Components | Phosphoglycerate mutase family protein, putative | ||||||
Keywords | HYDROLASE / Histidine phosphatase superfamily memeber / Phosphatase / cysteine biosynthetic pathway / BIOSYNTHETIC PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Entamoeba histolytica HM-1:IMSS-A (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kumari, P. / Gourinath, S. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2019 Title: Structural and functional characterisation of phosphoserine phosphatase, that plays critical role in the oxidative stress response in the parasite Entamoeba histolytica. Authors: Kumari, P. / Babuta, M. / Bhattacharya, A. / Gourinath, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zkk.cif.gz | 99.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zkk.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zkk_validation.pdf.gz | 496.4 KB | Display | wwPDB validaton report |
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Full document | 5zkk_full_validation.pdf.gz | 501.3 KB | Display | |
Data in XML | 5zkk_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 5zkk_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/5zkk ftp://data.pdbj.org/pub/pdb/validation_reports/zk/5zkk | HTTPS FTP |
-Related structure data
Related structure data | 5zr2C 4ij5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23771.080 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS-A (eukaryote) Gene: EHI7A_041450 / Plasmid: pET 28b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: N9V397 |
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-Non-polymers , 7 types, 229 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-144 / | #6: Chemical | #7: Chemical | #8: 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 Å3/Da / Density % sol: 59.02 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 0.1 M phosphate citrate buffer, pH 4.2, 4% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→94.55 Å / Num. obs: 39785 / % possible obs: 98.7 % / Redundancy: 14.6 % / CC1/2: 0.996 / Χ2: 1.305 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2002 / CC1/2: 0.802 / Χ2: 0.856 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IJ5 Resolution: 2→94.55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.077 Å2
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Refinement step | Cycle: 1 / Resolution: 2→94.55 Å
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