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- PDB-7x8j: Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (unl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7x8j | ||||||
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Title | Arabidopsis GDP-D-mannose pyrophosphorylase (VTC1) structure (unliganded) | ||||||
![]() | Mannose-1-phosphate guanylyltransferase 1 | ||||||
![]() | TRANSFERASE / ascorbic acid / nucleotide sugar / guanylyltransferase / Arabidopsis thaliana | ||||||
Function / homology | ![]() mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / cellulose biosynthetic process / cell wall mannoprotein biosynthetic process / GDP-mannose biosynthetic process / response to ammonium ion / response to jasmonic acid / response to ozone / L-ascorbic acid biosynthetic process / protein glycosylation ...mannose-1-phosphate guanylyltransferase / mannose-1-phosphate guanylyltransferase (GTP) activity / cellulose biosynthetic process / cell wall mannoprotein biosynthetic process / GDP-mannose biosynthetic process / response to ammonium ion / response to jasmonic acid / response to ozone / L-ascorbic acid biosynthetic process / protein glycosylation / response to salt stress / nucleotidyltransferase activity / response to heat / defense response to bacterium / GTP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, S. / Zhang, C. / Liu, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of Arabidopsis thaliana GDP-D-Mannose Pyrophosphorylase VITAMIN C DEFECTIVE 1. Authors: Zhang, C. / Zhao, S. / Li, Y.S. / He, C. / Wang, X. / Liu, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150 KB | Display | ![]() |
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PDB format | ![]() | 115.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.9 MB | Display | ![]() |
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Full document | ![]() | 5 MB | Display | |
Data in XML | ![]() | 26.3 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7x8kC ![]() 7d72S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 41340.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CYT1, EMB101, GMP1, HSN1, SOZ1, VTC1, At2g39770, T5I7.7 Production host: ![]() ![]() References: UniProt: O22287, mannose-1-phosphate guanylyltransferase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.5 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: bis-tris, PEG 3350, lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.798→50 Å / Num. obs: 21924 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 63.63 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.047 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2165 / CC1/2: 0.881 / Rpim(I) all: 0.31 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7D72 Resolution: 2.798→32.633 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 31.45 / 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: 106.53 Å2 / Biso mean: 63.7663 Å2 / Biso min: 37.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.798→32.633 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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