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- PDB-1nr5: Crystal structure of 3-dehydroquinate synthase (DHQS) in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1nr5 | ||||||
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Title | Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+, NAD and carbaphosphonate | ||||||
![]() | 3-DEHYDROQUINATE SYNTHASE | ||||||
![]() | LYASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / DHQS / CARBAPHOSPHONATE / CLOSED FORM / DOMAIN MOVEMENT / CYCLASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nichols, C.E. / Ren, J. / Lamb, H.K. / Hawkins, A.R. / Stammers, D.K. | ||||||
![]() | ![]() Title: Ligand-induced Conformational Changes and a Mechanism for Domain Closure in Aspergillus nidulans Dehydroquinate Synthase Authors: Nichols, C.E. / Ren, J. / Lamb, H.K. / Hawkins, A.R. / Stammers, D.K. #1: ![]() Title: Identification of many crystal forms of Aspergillus nidulans dehydroquinate synthase Authors: Nichols, C.E. / Ren, J. / Lamb, H. / Haldane, F. / Hawkins, A.R. / Stammers, D.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.9 KB | Display | ![]() |
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PDB format | ![]() | 136.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 35.4 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nrxC ![]() 1nuaC ![]() 1nvaC ![]() 1nvbC ![]() 1nvdC ![]() 1nveC ![]() 1nvfC ![]() 1dqsS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dimer, each monomer in the asymetric unit generating one dimer by symetry across a two fold axis. |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 42966.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 392 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/CRB.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NAD.gif)
![](data/chem/img/CRB.gif)
![](data/chem/img/CO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CO / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.04 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Ammonium Sulphate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 Details: Nichols, C.E., (2001) Acta Crystallogr., Sect.D, 57, 306. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 1, 1999 / Details: OSMIC MULTILAYER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 51528 / Num. obs: 48900 / % possible obs: 94.9 % / Observed criterion σ(I): -1.5 / Redundancy: 2.91 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.96 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 2.61 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8482 / % possible all: 92.5 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 96.9 % |
Reflection shell | *PLUS Lowest resolution: 2.18 Å / % possible obs: 96.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DQS Resolution: 2.1→27.22 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2963347.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 71.9463 Å2 / ksol: 0.32668 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→27.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.183 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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