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Yorodumi- PDB-5hud: Non-covalent complex of and DAHP synthase and chorismate mutase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hud | ||||||
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Title | Non-covalent complex of and DAHP synthase and chorismate mutase from Corynebacterium glutamicum with bound transition state analog | ||||||
Components |
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Keywords | TRANSFERASE/ISOMERASE / chorismate mutase / DAHP synthase / shikimate pathway / complex / Transferase-Isomerase complex | ||||||
Function / homology | Function and homology information chorismate metabolic process / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Burschowsky, D. / Heim, J.B. / Thorbjoernsrud, H.V. / Krengel, U. | ||||||
Funding support | Norway, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: Inter-Enzyme Allosteric Regulation of Chorismate Mutase in Corynebacterium glutamicum: Structural Basis of Feedback Activation by Trp. Authors: Burschowsky, D. / Thorbjornsrud, H.V. / Heim, J.B. / Fahrig-Kamarauskaite, J.R. / Wurth-Roderer, K. / Kast, P. / Krengel, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hud.cif.gz | 457.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hud.ent.gz | 376.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hud_validation.pdf.gz | 628.4 KB | Display | wwPDB validaton report |
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Full document | 5hud_full_validation.pdf.gz | 667 KB | Display | |
Data in XML | 5hud_validation.xml.gz | 90.3 KB | Display | |
Data in CIF | 5hud_validation.cif.gz | 123.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/5hud ftp://data.pdbj.org/pub/pdb/validation_reports/hu/5hud | HTTPS FTP |
-Related structure data
Related structure data | 5hubC 5hucC 5hueC 2w1aS 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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Unit cell |
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-Components
-Protein , 2 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 52150.395 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: Cgl2178 / Production host: Escherichia coli (E. coli) / Variant (production host): KA13 / References: UniProt: Q8NNL5 #2: Protein | Mass: 10065.521 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: Cgl0853 / Production host: Escherichia coli (E. coli) / Variant (production host): KA13 / References: UniProt: Q8NS29, chorismate mutase |
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-Non-polymers , 9 types, 898 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-PGE / #6: Chemical | ChemComp-MN / #7: Chemical | ChemComp-PO4 / #8: Chemical | ChemComp-TRP / #9: Chemical | ChemComp-PG4 / #10: Chemical | ChemComp-TSA / #11: 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: 3.45 Å3/Da / Density % sol: 64.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM imidazole/MES buffer, pH 6.5 30 mM each of ethylene glycol mix (di-ethylene glycol, tri-ethylene glycol, tetra-ethylene glycol, penta-ethylene glycol) 15% glycerol 15% PEG 4000 micro- ...Details: 100 mM imidazole/MES buffer, pH 6.5 30 mM each of ethylene glycol mix (di-ethylene glycol, tri-ethylene glycol, tetra-ethylene glycol, penta-ethylene glycol) 15% glycerol 15% PEG 4000 micro-seeded from badly diffracting crystals (approx. 8 AA resolution), in 100 mM Na-HEPES, pH 7.5, 200 mM LiSO4, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97239 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→131.99 Å / Num. obs: 190339 / % possible obs: 96.7 % / Redundancy: 2.95 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 4.79 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 2.24 % / Rmerge(I) obs: 1.763 / Mean I/σ(I) obs: 0.44 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W1A Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.867 / SU B: 10.127 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.215 / 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: 33.789 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→40 Å
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Refine LS restraints |
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