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Yorodumi- PDB-8hx7: Crystal structure of 4-amino-4-deoxychorismate synthase from Stre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hx7 | ||||||
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Title | Crystal structure of 4-amino-4-deoxychorismate synthase from Streptomyces venezuelae co-crystallized with L-glutamine | ||||||
Components | 4-amino-4-deoxychorismate synthase | ||||||
Keywords | TRANSFERASE / Synthase / Multi-domain / Chorismate | ||||||
Function / homology | Function and homology information aminodeoxychorismate synthase / 4-amino-4-deoxychorismate synthase activity / para-aminobenzoic acid biosynthetic process / folic acid-containing compound biosynthetic process / glutamine metabolic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces venezuelae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Nakamichi, Y. / Watanabe, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hx7.cif.gz | 524.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hx7.ent.gz | 432.8 KB | Display | PDB format |
PDBx/mmJSON format | 8hx7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8hx7_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8hx7_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8hx7_validation.xml.gz | 46.1 KB | Display | |
Data in CIF | 8hx7_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/8hx7 ftp://data.pdbj.org/pub/pdb/validation_reports/hx/8hx7 | HTTPS FTP |
-Related structure data
Related structure data | 8hx6C 8hx8C 8hx9C 1qdlS C: citing same article (ref.) S: Starting model for refinement |
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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
-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.) Streptomyces venezuelae (bacteria) / Gene: papA / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6L8Q5, aminodeoxychorismate synthase |
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-Non-polymers , 5 types, 155 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.19 Å3/Da / Density % sol: 43.93 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→49.31 Å / Num. obs: 98481 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 40.29 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 17.66 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 1.33 / Num. unique obs: 9639 / CC1/2: 0.616 / Rpim(I) all: 0.797 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QDL Resolution: 1.95→47.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 13.801 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.158 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.309 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→47.11 Å
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Refine LS restraints |
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