+Open data
-Basic information
Entry | Database: PDB / ID: 5ym0 | ||||||
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Title | The crystal structure of DHAD | ||||||
Components | Dihydroxy-acid dehydratase, chloroplastic | ||||||
Keywords | LYASE / weed herbicide resistance dehydatase | ||||||
Function / homology | Function and homology information dihydroxy-acid dehydratase / dihydroxy-acid dehydratase activity / embryo sac development / pollen development / root development / branched-chain amino acid biosynthetic process / hydro-lyase activity / valine biosynthetic process / isoleucine biosynthetic process / plastid ...dihydroxy-acid dehydratase / dihydroxy-acid dehydratase activity / embryo sac development / pollen development / root development / branched-chain amino acid biosynthetic process / hydro-lyase activity / valine biosynthetic process / isoleucine biosynthetic process / plastid / chloroplast stroma / amino acid biosynthetic process / response to salt stress / chloroplast / 2 iron, 2 sulfur cluster binding / copper ion binding / mitochondrion Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.842 Å | ||||||
Authors | Zang, X. / Huang, W.X. / Cheng, R. / Wu, L. / Zhou, J.H. / Tang, Y. / Yan, Y. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of DHAD Authors: Zang, X. / Huang, W.X. / Cheng, R. / Wu, L. / Zhou, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ym0.cif.gz | 220.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ym0.ent.gz | 181.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ym0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ym0_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 5ym0_full_validation.pdf.gz | 438.4 KB | Display | |
Data in XML | 5ym0_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 5ym0_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/5ym0 ftp://data.pdbj.org/pub/pdb/validation_reports/ym/5ym0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 67975.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DHAD, ILVD, At3g23940, F14O13.13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LIR4, dihydroxy-acid dehydratase | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.37 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M sodium acetate pH 5.5, 1.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.96422 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 14, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96422 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→50 Å / Num. obs: 55067 / % possible obs: 99.8 % / Redundancy: 10.7 % / Net I/σ(I): 22.6 |
-Processing
Software |
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Refinement | Resolution: 1.842→28.9 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.89
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.842→28.9 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: 37.082 Å / Origin y: -12.3852 Å / Origin z: -0.1633 Å
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Refinement TLS group | Selection details: all |