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Yorodumi- PDB-5e7z: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e7z | |||||||||
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Title | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis in complex with D/L-tryptophan and D-phenylalanine | |||||||||
Components | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase | |||||||||
Keywords | TRANSFERASE / shikimate pathway / allosteric regulation | |||||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / peptidoglycan-based cell wall / protein homooligomerization / manganese ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | |||||||||
Authors | Reichau, S. / Jiao, W. / Parker, E.J. | |||||||||
Funding support | New Zealand, 2items
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Citation | Journal: Plos One / Year: 2016 Title: Probing the Sophisticated Synergistic Allosteric Regulation of Aromatic Amino Acid Biosynthesis in Mycobacterium tuberculosis Using -Amino Acids. Authors: Reichau, S. / Blackmore, N.J. / Jiao, W. / Parker, E.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e7z.cif.gz | 355.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e7z.ent.gz | 291 KB | Display | PDB format |
PDBx/mmJSON format | 5e7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e7z_validation.pdf.gz | 509.8 KB | Display | wwPDB validaton report |
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Full document | 5e7z_full_validation.pdf.gz | 519.2 KB | Display | |
Data in XML | 5e7z_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 5e7z_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/5e7z ftp://data.pdbj.org/pub/pdb/validation_reports/e7/5e7z | HTTPS FTP |
-Related structure data
Related structure data | 5e2lC 5e40C 5e4nC 5e5gC 3nv8S 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 50828.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: aroG_1, ERS024751_03564, ERS094182_00944, ERS124362_02783 Production host: Escherichia coli (E. coli) References: UniProt: A0A0E8NFD1, UniProt: O53512*PLUS, 3-deoxy-7-phosphoheptulonate synthase |
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-Non-polymers , 7 types, 144 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: 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: 4.05 Å3/Da / Density % sol: 69.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 7.5, 1.5M AMMONIUM SULFATE, 12% V/V GLYCEROL. CRYSTALS WERE SOAKED IN THE SAME SOLUTION WITH AN ADDITIONAL 10% V/V GLYCEROL AND 0.25 MILLIM D- ...Details: CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL, PH 7.5, 1.5M AMMONIUM SULFATE, 12% V/V GLYCEROL. CRYSTALS WERE SOAKED IN THE SAME SOLUTION WITH AN ADDITIONAL 10% V/V GLYCEROL AND 0.25 MILLIM D-PHENYLALANINE AND 2.5 MILLIM TRYPTOPHAN |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2012 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.33→47.55 Å / Num. obs: 71044 / % possible obs: 100 % / Redundancy: 12.3 % / Net I/σ(I): 4.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3NV8 Resolution: 2.4→47.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.175 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.029 / 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: 35.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→47.55 Å
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