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Yorodumi- PDB-3qbe: Crystal structure of the 3-Dehydroquinate Synthase (aroB) from My... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qbe | ||||||
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Title | Crystal structure of the 3-Dehydroquinate Synthase (aroB) from Mycobacterium tuberculosis | ||||||
Components | 3-dehydroquinate synthase | ||||||
Keywords | LYASE / dehydroquinate synthase (DHQS) / shikimate pathway / Mycobacterium tuberculosis / nicotinamide adenine dinucleotide (NAD)-dependent enzyme / Rossmann-fold | ||||||
Function / homology | Function and homology information 3-dehydroquinate synthase / 3-dehydroquinate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / peptidoglycan-based cell wall / copper ion binding / nucleotide binding / zinc ion binding ...3-dehydroquinate synthase / 3-dehydroquinate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / peptidoglycan-based cell wall / copper ion binding / nucleotide binding / zinc ion binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Cheng, W.C. / Wen, Y.H. / Wang, W.C. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the 3-Dehydroquinate Synthase (aroB) from Mycobacterium tuberculosis Authors: Cheng, W.C. / Chen, T.J. / Wang, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qbe.cif.gz | 80.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qbe.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 3qbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/3qbe ftp://data.pdbj.org/pub/pdb/validation_reports/qb/3qbe | HTTPS FTP |
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-Related structure data
Related structure data | 3qbdS 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
#1: Protein | Mass: 38992.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: aroB, MRA_2566 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: A5U5N7, UniProt: P9WPX9*PLUS, 3-dehydroquinate synthase | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.8M sodium formate, 20% PEG 2000 MME, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→99.22 Å / Num. all: 23228 / Num. obs: 23186 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.07→2.14 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.65 / Num. unique all: 2309 / Rsym value: 0.492 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QBD Resolution: 2.07→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / ESU R Free: 0.183 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.514 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.124 Å / Total num. of bins used: 20
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