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Yorodumi- PDB-6bmb: Crystal structure of Arabidopsis Dehydroquinate dehydratase-shiki... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bmb | ||||||
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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 3-dehydrogenase (NADP+) activity / shikimate metabolic process / embryo development ending in seed dormancy / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chloroplast stroma / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process ...shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / shikimate metabolic process / embryo development ending in seed dormancy / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chloroplast stroma / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / 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 | 6bmb.cif.gz | 120.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bmb.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 6bmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/6bmb ftp://data.pdbj.org/pub/pdb/validation_reports/bm/6bmb | HTTPS FTP |
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-Related structure data
Related structure data | 6bmqC 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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2 |
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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: Thr381Gly Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: EMB3004, At3g06350, F24P17.18 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9SQT8, 3-dehydroquinate dehydratase, shikimate dehydrogenase (NADP+) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-TLA / | #4: Chemical | ChemComp-SKM / ( | #5: 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: 2.87 Å3/Da / Density % sol: 57.16 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 100 mM sodium citrate, pH 4.8, and 2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 10, 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→31.626 Å / Num. obs: 37904 / % possible obs: 99.23 % / Observed criterion σ(F): 0 / Redundancy: 1.8 % / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.038 / Rrim(I) all: 0.053 / Net I/σ(I): 9.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GPT Resolution: 2.077→31.626 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.78 Å2 / Biso mean: 35.7131 Å2 / Biso min: 18.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.077→31.626 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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