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Yorodumi- PDB-1dqs: CRYSTAL STRUCTURE OF DEHYDROQUINATE SYNTHASE (DHQS) COMPLEXED WIT... -
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-Basic information
Entry | Database: PDB / ID: 1dqs | ||||||
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Title | CRYSTAL STRUCTURE OF DEHYDROQUINATE SYNTHASE (DHQS) COMPLEXED WITH CARBAPHOSPHONATE, NAD+ AND ZN2+ | ||||||
Components | PROTEIN (3-DEHYDROQUINATE SYNTHASE) | ||||||
Keywords | LYASE / SHIKIMATE PATHWAY ENZYME / MULTI-STEP ENZYME / OXIDOREDUCTASE / PHOSPHATE ELIMINATION / INTRA MOLECULAR ALDOL CONDENSATION / NAD+ BINDING / ZN2+ BINDING / CYCLASE / AROMATIC AMINO ACID BIOSYNTHESIS | ||||||
Function / homology | Function and homology information 3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate kinase activity / shikimate dehydrogenase (NADP+) / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity ...3-dehydroquinate synthase / 3-dehydroquinate synthase activity / shikimate kinase / shikimate kinase activity / shikimate dehydrogenase (NADP+) / 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase 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 / SIRAS / Resolution: 1.8 Å | ||||||
Authors | Carpenter, E.P. / Hawkins, A.R. / Frost, J.W. / Brown, K.A. | ||||||
Citation | Journal: Nature / Year: 1998 Title: Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis. Authors: Carpenter, E.P. / Hawkins, A.R. / Frost, J.W. / Brown, K.A. #1: Journal: J.Am.Chem.Soc. / Year: 1998 Title: Reactivation of 3-Dehydroquinate Synthase by Lanthanide Cations Authors: Moore, J.D. / Skinner, M.A. / Swatman, D.R. / Hawkins, A.R. / Brown, K.A. #2: Journal: J.Am.Chem.Soc. / Year: 1997 Title: Cyclohexenyl and Cyclohexylidene Inhibitors of 3-Dehydroquinate Synthase: Active Site Interactions Relevant to Enzyme Mechanism and Inhibitor Design Authors: Montchamp, J.L. / Frost, J.W. #3: Journal: Biochem.J. / Year: 1994 Title: Efficient Independent Activity of a Monomeric, Monofunctional Dehydroquinate Synthase Derived from the N-Terminus of the Pentafunctional Arom Protein of Aspergillus Nidulans Authors: Moore, J.D. / Coggins, J.R. / Virden, R. / Hawkins, A.R. #4: Journal: J.Gen.Microbiol. / Year: 1993 Title: The Pre-Chorismate (Shikimate) and Quinate Pathways in Filamentous Fungi: Theoretical and Practical Aspects Authors: Hawkins, A.R. / Lamb, H.K. / Moore, J.D. / Charles, I.G. / Roberts, C.F. #5: Journal: Biochem.J. / Year: 1992 Title: Overproduction in Escherichia Coli of the Dehydroquinate Synthase Domain of the Aspergillus Nidulans Pentafunctional Arom Protein Authors: Van Den Hombergh, J.P. / Moore, J.D. / Charles, I.G. / Hawkins, A.R. #6: Journal: Biochemistry / Year: 1989 Title: Dehydroquinate Synthase: The Use of Substrate Analogues to Probe the Early Steps of the Catalyzed Reaction Authors: Bender, S.L. / Widlanski, T. / Knowles, J.R. #7: Journal: J.Biol.Chem. / Year: 1963 Title: The Enzymatic Conversion of 3-Deoxy-D-Arabino-Heptulosinic Acid 7-Phosphate to 5-Dehydroquinate Authors: Srinivasen, P.R. / Rothchild, J. / Sprinson, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dqs.cif.gz | 172.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dqs.ent.gz | 135.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/1dqs ftp://data.pdbj.org/pub/pdb/validation_reports/dq/1dqs | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42966.535 Da / Num. of mol.: 2 Fragment: N-TERMINAL DOMAIN OF THE PENTAFUNCTIONAL AROM PROTEIN Source method: isolated from a genetically manipulated source Details: DHQS IS A DIMER, WITH ONE NAD+, ONE ZN2+ AND ONE SUBSTRATE ANALOGUE INHIBITOR (CARBAPHOSPHONATE, CRB) BOUND PER MONOMER Source: (gene. exp.) Emericella nidulans (mold) / Strain: R153 / Cellular location: CYTOPLASM / Gene: PART OF AROMA / Plasmid: PTR51 / Cellular location (production host): CYTOPLASM / Gene (production host): PART OF AROMA / Production host: Escherichia coli (E. coli) Strain (production host): GLW38 (AROB-) FROM THE GLASGOW CULTURE COLLECTION References: UniProt: P07547, EC: 4.6.1.3 |
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-Non-polymers , 5 types, 725 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Chemical | #6: 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: 1.9 Å3/Da / Density % sol: 32 % |
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Crystal grow | pH: 6.8 / Details: pH 6.8 |
Crystal | *PLUS |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25 Å / Num. obs: 79632 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 19.22 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.3 / % possible all: 84.8 |
Reflection | *PLUS Num. measured all: 297189 |
Reflection shell | *PLUS % possible obs: 84.8 % |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 20.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.249 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |