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Yorodumi- PDB-1nvb: Crystal structure of 3-dehydroquinate synthase (DHQS) in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nvb | ||||||
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Title | Crystal structure of 3-dehydroquinate synthase (DHQS) in complex with ZN2+ and carbaphosphonate | ||||||
Components | 3-DEHYDROQUINATE SYNTHASE | ||||||
Keywords | LYASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / DHQS / CLOSED FORM / FORM C / DOMAIN MOVEMENT / CYCLASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Nichols, C.E. / Ren, J. / Lamb, H.K. / Hawkins, A.R. / Stammers, D.K. | ||||||
Citation | Journal: J.MOL.BIOL. / Year: 2003 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: Journal: Acta Crystallogr.,Sect.D / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nvb.cif.gz | 166.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nvb.ent.gz | 130.6 KB | Display | PDB format |
PDBx/mmJSON format | 1nvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/1nvb ftp://data.pdbj.org/pub/pdb/validation_reports/nv/1nvb | HTTPS FTP |
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-Related structure data
Related structure data | 1nr5SC 1nrxC 1nuaC 1nvaC 1nvdC 1nveC 1nvfC S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The biological assembly is a dimer, each monomer in the asymetric unit generating one dimer by symetry across a two fold axis. |
-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.) Emericella nidulans (mold) / Gene: AROMA / Plasmid: PTR51 / Production host: Escherichia coli (E. coli) / Strain (production host): GLW38 (AROB-) / References: UniProt: P07547, 3-dehydroquinate synthase |
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-Non-polymers , 5 types, 216 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NAD / | #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: 2.32 Å3/Da / Density % sol: 46.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: AMMONIUM SULPHATE, COBALT CHLORIDE, HEPES, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal grow | *PLUS Method: unknown |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
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: 2.7→30 Å / Num. all: 23148 / Num. obs: 22060 / % possible obs: 95.3 % / Observed criterion σ(I): -1.5 / Redundancy: 4.06 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.181 / Net I/σ(I): 4.18 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.24 / Num. unique all: 2264 / % possible all: 93.1 |
Reflection | *PLUS Lowest resolution: 30 Å |
Reflection shell | *PLUS % possible obs: 92.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NR5 Resolution: 2.7→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2652813.04 / 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: 37.9116 Å2 / ksol: 0.349825 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.205 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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