+Open data
-Basic information
Entry | Database: PDB / ID: 8pne | ||||||
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Title | E.coli YihX Wild Type Apo | ||||||
Components | Alpha-D-glucose 1-phosphate phosphatase YihX | ||||||
Keywords | HYDROLASE / Apo / Phosphatase | ||||||
Function / homology | Function and homology information glucose-1-phosphatase / glucose-1-phosphatase activity / manganese ion binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli str. K-12 substr. MG1655 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zappala, D. / Baumann, P. / Jin, Y. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Apo structure of E.coli YihX Wild Type Authors: Zappala, D. / Baumann, P. / Jin, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pne.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pne.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 8pne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pne_validation.pdf.gz | 450.3 KB | Display | wwPDB validaton report |
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Full document | 8pne_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 8pne_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 8pne_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/8pne ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pne | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23829.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: yihX, b3885, JW5566 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A8Y3, glucose-1-phosphatase |
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-Non-polymers , 6 types, 172 molecules
#2: Chemical | ChemComp-PEG / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-CA / | #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 4.16 Å3/Da / Density % sol: 70.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20-60 mg/mL YihX protein in the buffer of Tris-HCl 25 mM pH 7.5, NaCl 150 mM, MgCl2 20 mM, NaF 30 mM, was mixed 1:1 ratio with the precipitant containing MES 55.5 mM, imidazole 44.5 mM pH 6. ...Details: 20-60 mg/mL YihX protein in the buffer of Tris-HCl 25 mM pH 7.5, NaCl 150 mM, MgCl2 20 mM, NaF 30 mM, was mixed 1:1 ratio with the precipitant containing MES 55.5 mM, imidazole 44.5 mM pH 6.5, 30 mM MgCl2, 30 mM CaCl2, 20% glycerol, 10% PEG4000, 20% PEG500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 31, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→70.2 Å / Num. obs: 31737 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.998 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.9→1.94 Å / Num. unique obs: 2009 / CC1/2: 0.837 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→70.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.822 / SU ML: 0.121 / Cross valid method: FREE R-VALUE / ESU R: 0.111 / ESU R Free: 0.111 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→70.2 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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