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Yorodumi- PDB-2qji: M. jannaschii ADH synthase complexed with dihydroxyacetone phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qji | ||||||
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Title | M. jannaschii ADH synthase complexed with dihydroxyacetone phosphate and glycerol | ||||||
Components | Putative aldolase MJ0400 | ||||||
Keywords | LYASE / beta-alpha barrel | ||||||
Function / homology | Function and homology information 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase / transketolase or transaldolase activity / hydro-lyase activity / fructose-bisphosphate aldolase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ealick, S.E. / Morar, M. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Structure of 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid synthase, a catalyst in the archaeal pathway for the biosynthesis of aromatic amino acids. Authors: Morar, M. / White, R.H. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qji.cif.gz | 982.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qji.ent.gz | 842.2 KB | Display | PDB format |
PDBx/mmJSON format | 2qji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/2qji ftp://data.pdbj.org/pub/pdb/validation_reports/qj/2qji | HTTPS FTP |
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-Related structure data
-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
#1: Protein | Mass: 29719.182 Da / Num. of mol.: 20 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Production host: Escherichia coli (E. coli) References: UniProt: Q57843, Lyases; Carbon-oxygen lyases; Hydro-lyases #2: Chemical | ChemComp-13P / #3: Chemical | ChemComp-GOL / #4: 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: 2.5 Å3/Da / Density % sol: 50.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 6% 1,4-butanediol, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→41.19 Å / Num. all: 132360 / Num. obs: 125135 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.6 Å2 |
Reflection shell | Resolution: 2.8→2.98 Å / % possible all: 77.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→41.19 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 222073.65 / Data cutoff high rms absF: 222073.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.1268 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→41.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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