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Yorodumi- PDB-5e40: 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5.0E+40 | |||||||||
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Title | 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis with D-tyrosine bound in the phenylalanine binding site | |||||||||
Components | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase | |||||||||
Keywords | TRANSFERASE / amino acid / allosteric regulation / shikimate pathway / 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase | |||||||||
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: 2.05 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 | 5e40.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e40.ent.gz | 159.2 KB | Display | PDB format |
PDBx/mmJSON format | 5e40.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e40_validation.pdf.gz | 473.2 KB | Display | wwPDB validaton report |
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Full document | 5e40_full_validation.pdf.gz | 482.5 KB | Display | |
Data in XML | 5e40_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 5e40_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/5e40 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/5e40 | HTTPS FTP |
-Related structure data
Related structure data | 5e2lC 5e4nC 5e5gC 5e7zC 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 on special symmetry positions |
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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 , 5 types, 547 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: 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 Å3/Da / Density % sol: 69.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Tris-HCl, pH 7.5, 1.5 M ammonium sulfate, 12% v/v glycerol. For soaking, 0.2 microliters of a 10 mM D-Tyr stock solution was added to equilibrated 2 microliter droplets at 48 hours and ...Details: 0.1 M Tris-HCl, pH 7.5, 1.5 M ammonium sulfate, 12% v/v glycerol. For soaking, 0.2 microliters of a 10 mM D-Tyr stock solution was added to equilibrated 2 microliter droplets at 48 hours and 24 hours before crystal freezing, respectively |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 4, 2012 | |||||||||||||||||||||||||||
Radiation | Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.05→19.85 Å / Num. obs: 101083 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.056 / Net I/σ(I): 11.8 / Num. measured all: 762663 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-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: 2.05→19.85 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1829 / WRfactor Rwork: 0.1726 / FOM work R set: 0.8952 / SU B: 2.831 / SU ML: 0.078 / SU R Cruickshank DPI: 0.0295 / SU Rfree: 0.0259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.026 / 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 max: 99.95 Å2 / Biso mean: 27.469 Å2 / Biso min: 15.97 Å2
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Refinement step | Cycle: final / Resolution: 2.05→19.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20
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