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Yorodumi- PDB-6bmq: Crystal structure of Arabidopsis Dehydroquinate dehydratase-shiki... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bmq | ||||||
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Title | Crystal structure of Arabidopsis Dehydroquinate dehydratase-shikimate dehydrogenase (T381G mutant) in complex with tartrate and shikimate | ||||||
Components | Bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase, chloroplastic | ||||||
Keywords | OXIDOREDUCTASE / Arabidopsis Shikimate dehydrogenase / NADP+ / Tartrate / shikimate | ||||||
Function / homology | Function and homology information shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / embryo development ending in seed dormancy / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / chloroplast stroma / amino acid biosynthetic process ...shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / embryo development ending in seed dormancy / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / chloroplast stroma / amino acid biosynthetic process / chloroplast / NADP binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.077 Å | ||||||
Authors | Christendat, D. / Peek, J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Plant J. / Year: 2018 Title: Structural and biochemical approaches uncover multiple evolutionary trajectories of plant quinate dehydrogenases. Authors: Gritsunov, A. / Peek, J. / Diaz Caballero, J. / Guttman, D. / Christendat, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bmq.cif.gz | 119.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bmq.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 6bmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bmq_validation.pdf.gz | 461.5 KB | Display | wwPDB validaton report |
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Full document | 6bmq_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 6bmq_validation.xml.gz | 23 KB | Display | |
Data in CIF | 6bmq_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/6bmq ftp://data.pdbj.org/pub/pdb/validation_reports/bm/6bmq | HTTPS FTP |
-Related structure data
Related structure data | 6bmbC 2gptS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 57044.910 Da / Num. of mol.: 1 / Mutation: T381G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EMB3004, At3g06350, F24P17.18 / Production host: Escherichia coli (E. coli) References: UniProt: Q9SQT8, 3-dehydroquinate dehydratase, shikimate dehydrogenase (NADP+) | ||||
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#2: Chemical | #3: Chemical | ChemComp-QIC / ( | #4: 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: 2.86 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium citrate, pH 4.8, and 2 M ammonium sulfate 20mM quinate 15mg/mL protein |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.077→31.66 Å / Num. obs: 38271 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 2 % / Biso Wilson estimate: 28.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03826 / Rpim(I) all: 0.038 / Rrim(I) all: 0.054 / Net I/σ(I): 13.5 |
Reflection scale | Group code: 1 |
Reflection shell | Resolution: 2.077→2.151 Å / Rmerge(I) obs: 0.3356 / Num. measured obs: 7400 / Num. unique all: 3805 / CC1/2: 0.727 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GPT Resolution: 2.077→31.656 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.34 / 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: 2.077→31.656 Å
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Refine LS restraints |
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LS refinement shell |
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