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Yorodumi- PDB-2zu7: Crystal structure of mannosyl-3-phosphoglycerate synthase from Py... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zu7 | ||||||
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Title | Crystal structure of mannosyl-3-phosphoglycerate synthase from Pyrococcus horikoshii | ||||||
Components | Mannosyl-3-phosphoglycerate synthase | ||||||
Keywords | TRANSFERASE / GT-A fold / glycosyltransferase / GT55 / Cytoplasm / Magnesium | ||||||
Function / homology | Function and homology information mannosyl-3-phosphoglycerate synthase / mannosyl-3-phosphoglycerate synthase activity / mannosylglycerate biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Kawamura, T. / Watanabe, N. / Tanaka, I. | ||||||
Citation | Journal: To be Published Title: Crystal structure of mannosyl-3-phosphoglycerate synthase from Pyrococcus horikoshii Authors: Kawamura, T. / Watanabe, N. / Tanaka, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zu7.cif.gz | 148 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zu7.ent.gz | 125.6 KB | Display | PDB format |
PDBx/mmJSON format | 2zu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zu7_validation.pdf.gz | 444 KB | Display | wwPDB validaton report |
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Full document | 2zu7_full_validation.pdf.gz | 474.7 KB | Display | |
Data in XML | 2zu7_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | 2zu7_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/2zu7 ftp://data.pdbj.org/pub/pdb/validation_reports/zu/2zu7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45977.918 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0927 / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: O58689, mannosyl-3-phosphoglycerate synthase #2: 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: 2.12 Å3/Da / Density % sol: 42.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 30% MPD, 0.05M sodium acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2007 |
Radiation | Monochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 26230 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 38.8 Å2 / Rsym value: 0.07 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 9.5 / Num. unique all: 2404 / Rsym value: 0.144 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→29.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1588512.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.9615 Å2 / ksol: 0.300717 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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