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Yorodumi- PDB-5e5g: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with D-trypt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e5g | |||||||||
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Title | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with D-tryptophan bound in the tryptophan and phenylalanine binding sites | |||||||||
Components | 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase | |||||||||
Keywords | TRANSFERASE / allosteric regulation / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / shikimate pathway | |||||||||
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: 1.95 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 | 5e5g.cif.gz | 369.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e5g.ent.gz | 300.9 KB | Display | PDB format |
PDBx/mmJSON format | 5e5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e5g_validation.pdf.gz | 466.4 KB | Display | wwPDB validaton report |
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Full document | 5e5g_full_validation.pdf.gz | 472.8 KB | Display | |
Data in XML | 5e5g_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 5e5g_validation.cif.gz | 58.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/5e5g ftp://data.pdbj.org/pub/pdb/validation_reports/e5/5e5g | HTTPS FTP |
-Related structure data
Related structure data | 5e2lC 5e40C 5e4nC 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
#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 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-DTR / #5: 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: 3.97 Å3/Da / Density % sol: 69.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 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 10 MM D-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: Apr 14, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.95→47.25 Å / Num. obs: 116470 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.047 / Net I/σ(I): 14.1 / Num. measured all: 1300419 | |||||||||||||||||||||||||||
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: 1.95→47.25 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.1645 / FOM work R set: 0.9079 / SU B: 3.219 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0247 / SU Rfree: 0.0224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.02 / 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: 105.6 Å2 / Biso mean: 31.686 Å2 / Biso min: 14.24 Å2
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Refinement step | Cycle: final / Resolution: 1.95→47.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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