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- PDB-8hx9: Crystal structure of 4-amino-4-deoxychorismate synthase from Stre... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hx9 | ||||||
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Title | Crystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae with chorismate | ||||||
![]() | 4-amino-4-deoxychorismate synthase | ||||||
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Function / homology | ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakamichi, Y. / Watanabe, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the allosteric pathway of 4-amino-4-deoxychorismate synthase. Authors: Nakamichi, Y. / Kobayashi, J. / Toyoda, K. / Suda, M. / Hiraga, K. / Inui, M. / Watanabe, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 523.4 KB | Display | ![]() |
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PDB format | ![]() | 430.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8hx6C ![]() 8hx7C ![]() 8hx8C ![]() 1qdlS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 76744.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 76 molecules ![](data/chem/img/TRP.gif)
![](data/chem/img/ISJ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ISJ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ChemComp-ISJ / ( | ![]() #4: Chemical | ChemComp-GOL / | ![]() #5: Chemical | #6: Chemical | ChemComp-FMT / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.05 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 51% (v/v) Tacsimate, 0.1 M Bis-tris propane (pH 7.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.03→47.48 Å / Num. obs: 88867 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 45.02 Å2 / CC1/2: 1 / Rpim(I) all: 0.022 / Net I/σ(I): 20.87 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.41 / Num. unique obs: 8752 / CC1/2: 1 / Rpim(I) all: 0.618 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1QDL Resolution: 2.03→47.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 30.186 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.689 Å2
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Refinement step | Cycle: 1 / Resolution: 2.03→47.47 Å
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Refine LS restraints |
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