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Yorodumi- PDB-1sg6: Crystal structure of Aspergillus nidulans 3-dehydroquinate syntha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sg6 | ||||||
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Title | Crystal structure of Aspergillus nidulans 3-dehydroquinate synthase (AnDHQS) in complex with Zn2+ and NAD+, at 1.7D | ||||||
Components | Pentafunctional AROM polypeptide | ||||||
Keywords | LYASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / DHQS / OPEN FORM / FORM J / DOMAIN MOVEMENT / CYCLASE | ||||||
Function / homology | Function and homology information 3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate dehydrogenase (NADP+) / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity ...3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate dehydrogenase (NADP+) / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Emericella nidulans (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Model details | Open form with co-factor, crystal form J, derived from turnover experiment. | ||||||
Authors | Nichols, C.E. / Hawkins, A.R. / Stammers, D.K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of the 'open' form of Aspergillus nidulans 3-dehydroquinate synthase at 1.7 A resolution from crystals grown following enzyme turnover. Authors: Nichols, C.E. / Hawkins, A.R. / Stammers, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sg6.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sg6.ent.gz | 148.2 KB | Display | PDB format |
PDBx/mmJSON format | 1sg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/1sg6 ftp://data.pdbj.org/pub/pdb/validation_reports/sg/1sg6 | HTTPS FTP |
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-Related structure data
Related structure data | 1nveS S: Starting model for refinement |
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Similar 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 42966.535 Da / Num. of mol.: 2 Fragment: N-Terminal Domain Of The Pentafunctional Arom Protein (3-dehydroquinate synthase) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (mold) / Gene: AROMA, AROM / Plasmid: PTRC99A PTR51 / Production host: Escherichia coli (E. coli) Strain (production host): GLW38 (AROB-) FROM THE GLASGOW CULTURE COLLECTION References: UniProt: P07547, 3-dehydroquinate synthase #2: Chemical | #3: Chemical | #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: 2.54 Å3/Da / Density % sol: 51.15 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: PEG 3350, lithium sulphate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 90933 / Observed criterion σ(I): -1.5 / Redundancy: 7.2 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 13.67 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 1.55 / Num. measured all: 4557 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NVE Resolution: 1.7→30 Å / Cross valid method: THROUGHOUT / σ(I): -1.5 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.73 Å / Rfactor Rfree error: 0.016
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