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Yorodumi- PDB-8e0x: DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8e0x | ||||||||||||||||||
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Title | DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase complexed with Mn(II), PEP, and Pi in unbound:(bound)2:other Conformations | ||||||||||||||||||
Components | Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive | ||||||||||||||||||
Keywords | LYASE / DAHP synthase inhibitor / DAHP oxime complex | ||||||||||||||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||||||||||||||
Authors | Berti, P.J. / Junop, M.S. / Grainger, R. | ||||||||||||||||||
Funding support | Canada, 5items
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Citation | Journal: Biochemistry / Year: 2022 Title: Role of Half-of-Sites Reactivity and Inter-Subunit Communications in DAHP Synthase Catalysis and Regulation. Authors: Balachandran, N. / Grainger, R.A. / Rob, T. / Liuni, P. / Wilson, D.J. / Junop, M.S. / Berti, P.J. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e0x.cif.gz | 588.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e0x.ent.gz | 463.6 KB | Display | PDB format |
PDBx/mmJSON format | 8e0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e0x_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 8e0x_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 8e0x_validation.xml.gz | 58.6 KB | Display | |
Data in CIF | 8e0x_validation.cif.gz | 86.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/8e0x ftp://data.pdbj.org/pub/pdb/validation_reports/e0/8e0x | HTTPS FTP |
-Related structure data
Related structure data | 8e0sC 8e0tC 8e0uC 8e0vC 8e0yC 8e0zC 5cksS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38116.555 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: aroG, b0754, JW0737 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) References: UniProt: P0AB91, 3-deoxy-7-phosphoheptulonate synthase #2: Chemical | #3: Chemical | ChemComp-PEP / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.49 Å3/Da / Density % sol: 50.56 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M trilithium citrate tetrahydrate, 10% (w/v) PEG 3350, 5 mM DAHP oxime, 5 mM phosphoenolpyruvate, 5 mM erythrose 4-pohsphate, 30% (v/v) ethylene glycol, 1:1:0.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→67.65 Å / Num. obs: 105376 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03 / Rrim(I) all: 0.058 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.97→2.05 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5157 / CC1/2: 0.884 / Rpim(I) all: 0.254 / Rrim(I) all: 0.492 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CKS Resolution: 1.97→43.48 Å / SU ML: 0.1702 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4764 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→43.48 Å
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Refine LS restraints |
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LS refinement shell |
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