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Yorodumi- PDB-2b7o: The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b7o | ||||||
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Title | The Structure of 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase from Mycobacterium tuberculosis | ||||||
Components | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG | ||||||
Keywords | TRANSFERASE / Mycobacterium tuberculosis / DAH7PS synthase / Shikimate pathway / aromatic biosynthesis / evolutionary relationships / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB | ||||||
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 / SAD / Resolution: 2.3 Å | ||||||
Authors | Webby, C.J. / Baker, H.M. / Lott, J.S. / Baker, E.N. / Parker, E.J. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes Authors: Webby, C.J. / Baker, H.M. / Lott, J.S. / Baker, E.N. / 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 | 2b7o.cif.gz | 190.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b7o.ent.gz | 158.3 KB | Display | PDB format |
PDBx/mmJSON format | 2b7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b7o_validation.pdf.gz | 622.3 KB | Display | wwPDB validaton report |
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Full document | 2b7o_full_validation.pdf.gz | 646.6 KB | Display | |
Data in XML | 2b7o_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 2b7o_validation.cif.gz | 55 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/2b7o ftp://data.pdbj.org/pub/pdb/validation_reports/b7/2b7o | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-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: 51438.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2178c / Plasmid: pProExHTa / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 (DE3) References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase |
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-Non-polymers , 5 types, 343 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CE1 / | #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: 3.9 Å3/Da / Density % sol: 68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20mM BTP, 150mM NaCl, 0.5mM TCEP, 0.005% v/v Thesit, 0.2mM PEP, 0.1mM MnCl2, 0.1M Na HEPES, 0.8M NaK phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 23, 2004 / Details: Double-crystal, Si(111) |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 70357 / Num. obs: 70357 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 3.9 / Num. unique all: 6984 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→47.04 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.489 / SU ML: 0.113 / Isotropic thermal model: Individual atoms / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.194 / ESU R Free: 0.174 / 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: 43.524 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→47.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.299→2.359 Å / Total num. of bins used: 20
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