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Yorodumi- PDB-7ef7: Crystal Structure of Xanthosine monophosphate phosphatase complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ef7 | ||||||
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Title | Crystal Structure of Xanthosine monophosphate phosphatase complex with XMP | ||||||
Components | At2g32150/F22D22.10 | ||||||
Keywords | HYDROLASE / XMPase | ||||||
Function / homology | Function and homology information xanthosine biosynthetic process / response to water deprivation / response to abscisic acid / XMP 5'-nucleosidase activity / purine nucleoside catabolic process / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Yang, S. / Rhee, S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Initiation of cytosolic plant purine nucleotide catabolism involves a monospecific xanthosine monophosphate phosphatase. Authors: Heinemann, K.J. / Yang, S.Y. / Straube, H. / Medina-Escobar, N. / Varbanova-Herde, M. / Herde, M. / Rhee, S. / Witte, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ef7.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ef7.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ef7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/7ef7 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/7ef7 | HTTPS FTP |
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-Related structure data
Related structure data | 7ef6SC 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
#1: Protein | Mass: 27830.928 Da / Num. of mol.: 1 / Fragment: UNP residues 1-250 / Mutation: D12A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g32150, At2g32150/F22D22.10, F22D22.10, F22D22_10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9SKY5 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-XMP / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES (pH 7.0) 18%(w/v) PEG12000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 37816 / % possible obs: 98.3 % / Redundancy: 3.5 % / CC1/2: 0.989 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.5→1.53 Å / CC1/2: 0.989 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EF6 Resolution: 1.5→25.402 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.29 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→25.402 Å
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Refine LS restraints |
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LS refinement shell |
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