+Open data
-Basic information
Entry | Database: PDB / ID: 5wwd | ||||||
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Title | Crystal structure of AtNUDX1 | ||||||
Components | Nudix hydrolase 1 | ||||||
Keywords | HYDROLASE / NUDX1 / Arabidopsis thaliana / apo | ||||||
Function / homology | Function and homology information dihydroneopterin triphosphate diphosphatase / dihydroneopterin triphosphate pyrophosphohydrolase activity / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / 8-oxo-dGTP diphosphatase / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA damage response ...dihydroneopterin triphosphate diphosphatase / dihydroneopterin triphosphate pyrophosphohydrolase activity / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / 8-oxo-dGTP diphosphatase / dGTP catabolic process / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / DNA damage response / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.386 Å | ||||||
Authors | Liu, J. / Guan, Z. / Yan, L. / Zou, T. / Yin, P. | ||||||
Citation | Journal: Mol Plant / Year: 2018 Title: Structural Insights into the Substrate Recognition Mechanism of Arabidopsis GPP-Bound NUDX1 for Noncanonical Monoterpene Biosynthesis. Authors: Liu, J. / Guan, Z. / Liu, H. / Qi, L. / Zhang, D. / Zou, T. / Yin, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wwd.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wwd.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 5wwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wwd_validation.pdf.gz | 467.9 KB | Display | wwPDB validaton report |
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Full document | 5wwd_full_validation.pdf.gz | 470.8 KB | Display | |
Data in XML | 5wwd_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 5wwd_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/5wwd ftp://data.pdbj.org/pub/pdb/validation_reports/ww/5wwd | HTTPS FTP |
-Related structure data
Related structure data | 5gp0SC 5wy6C 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: 16582.779 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NUDT1, NUDX1, At1g68760, F14K14.13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q9CA40, 8-oxo-dGTP diphosphatase, dihydroneopterin triphosphate diphosphatase, NAD+ diphosphatase |
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-Non-polymers , 5 types, 395 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-2ME / | #4: Chemical | ChemComp-NH4 / | #5: Chemical | ChemComp-MG / #6: 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: 2.49 Å3/Da / Density % sol: 50.68 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: Sodium acetate trihydrate, PEG 2000, Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: CCD / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.356→41.59 Å / Num. obs: 458092 / % possible obs: 99.9 % / Redundancy: 6.3 % / Net I/σ(I): 25.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GP0 Resolution: 1.386→39.12 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.62 / 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: 1.386→39.12 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.3619 Å / Origin y: 60.0944 Å / Origin z: 1.4327 Å
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Refinement TLS group | Selection details: all |