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- PDB-1nvf: 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: 1nvf | ||||||
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Title | Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+, ADP and carbaphosphonate | ||||||
![]() | 3-DEHYDROQUINATE SYNTHASE | ||||||
![]() | LYASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / DHQS / CLOSED FORM / FORM H / 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 | ![]() | 247 KB | Display | ![]() |
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PDB format | ![]() | 197 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 50.7 KB | Display | |
Data in CIF | ![]() | 70.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nr5SC ![]() 1nrxC ![]() 1nuaC ![]() 1nvaC ![]() 1nvbC ![]() 1nvdC ![]() 1nveC S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dimer, chains A and B form one crystallographic dimer equivalent to this biological dimer and chain C lies across a crystallographic 2-fold generating a 2nd homo-symetric biological dimer. |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 42966.535 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 455 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/CRB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/CRB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.04 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG6000, DMSO, ETHYLENE GLYCOL, MEGA7, HEPES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 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: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 1, 2000 / Details: OSMIC MULTILAYER |
Radiation | Monochromator: OSMIC MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 29198 / Num. obs: 27530 / % possible obs: 94.7 % / Observed criterion σ(I): -1.5 / Redundancy: 3.12 % / Biso Wilson estimate: 53.4 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.28 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.37 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.17 / Num. unique all: 2390 / % possible all: 86.7 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 40 Å / % possible obs: 94.5 % / Redundancy: 3.46 % / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 81.4 % / Redundancy: 2.67 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.04 |
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Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 1NR5 Resolution: 2.8→26.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1921937.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.8721 Å2 / ksol: 0.285256 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→26.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 40 Å / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.3 |