+Open data
-Basic information
Entry | Database: PDB / ID: 8ikz | ||||||
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Title | The mutant structure of DHAD | ||||||
Components | Dihydroxy-acid dehydratase, chloroplastic | ||||||
Keywords | LYASE / [2Fe-2S] cluster / mutant / BCAA biosynthetic pathway | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Zhou, J. / Zang, X. / Tang, Y. / Yan, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: The mutant structure of DHAD Authors: Zhou, J. / Zang, X. / Tang, Y. / Yan, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ikz.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ikz.ent.gz | 98.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ikz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ikz_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8ikz_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8ikz_validation.xml.gz | 25.4 KB | Display | |
Data in CIF | 8ikz_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/8ikz ftp://data.pdbj.org/pub/pdb/validation_reports/ik/8ikz | HTTPS FTP |
-Related structure data
Related structure data | 8hs0C 5ze4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 61342.094 Da / Num. of mol.: 1 / Mutation: V496W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DHAD, At3g23940, F14O13.13 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9LIR4, dihydroxy-acid dehydratase |
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-Non-polymers , 5 types, 391 molecules
#2: Chemical | ChemComp-GOL / |
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#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-FES / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 2.5 Å3/Da / Density % sol: 50.75 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M sodium acetate pH 5.0, 1.5 M ammonium sulfate PH range: 4.5-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→47.53 Å / Num. obs: 62203 / % possible obs: 98.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.08 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.75→1.78 Å / Rmerge(I) obs: 0.788 / Num. unique obs: 3414 / CC1/2: 0.666 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZE4 Resolution: 1.75→37.6 Å / SU ML: 0.1885 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0048 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→37.6 Å
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Refine LS restraints |
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LS refinement shell |
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