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Yorodumi- PDB-5ex4: 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ex4 | |||||||||
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Title | 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with tryptophan in all three allosteric binding sites | |||||||||
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: 2.25 Å | |||||||||
Authors | Reichau, S. / Jiao, W. / Blackmore, N.J. / Hutton, R.D. / Parker, E.J. | |||||||||
Funding support | New Zealand, 2items
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Citation | Journal: to be published Title: 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with tryptophan in all three allosteric binding sites 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 | 5ex4.cif.gz | 214.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ex4.ent.gz | 169.1 KB | Display | PDB format |
PDBx/mmJSON format | 5ex4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ex4_validation.pdf.gz | 495.5 KB | Display | wwPDB validaton report |
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Full document | 5ex4_full_validation.pdf.gz | 504.6 KB | Display | |
Data in XML | 5ex4_validation.xml.gz | 42.4 KB | Display | |
Data in CIF | 5ex4_validation.cif.gz | 62.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/5ex4 ftp://data.pdbj.org/pub/pdb/validation_reports/ex/5ex4 | HTTPS FTP |
-Related structure data
Related structure data | 2b7oS S: Starting model for refinement |
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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, 724 molecules
#2: Chemical | #3: Chemical | ChemComp-TRP / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | ChemComp-CL / | #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: 3.98 Å3/Da / Density % sol: 69.11 % |
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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, 1.5 M AMMONIUM SULFATE, 12% V/V GLYCEROL, 1 MILLIM L-TRYPTOPHAN |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9357 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9357 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.25→44.24 Å / Num. all: 76066 / Num. obs: 76066 / % possible obs: 100 % / Redundancy: 10.8 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.131 / Rsym value: 0.125 / Net I/av σ(I): 4.789 / Net I/σ(I): 14.2 / Num. measured all: 818010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 2B7O Resolution: 2.25→44.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.1428 / FOM work R set: 0.9249 / SU B: 2.677 / SU ML: 0.07 / SU R Cruickshank DPI: 0.0308 / SU Rfree: 0.0277 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 140.03 Å2 / Biso mean: 26.286 Å2 / Biso min: 7.78 Å2
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Refinement step | Cycle: final / Resolution: 2.25→44.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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