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Yorodumi- PDB-3nv8: The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nv8 | ||||||
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Title | The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in complex with phosphoenol pyruvate and manganese (thesit-free) | ||||||
Components | Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG | ||||||
Keywords | TRANSFERASE / DAH7P synthase / Shikimate pathway / Aromatic amino-acid biosynthesis / Evolutionary relationships / Augmented TIM-barrel structure / TIM barrel / Aldolase / Cytosol | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Parker, E.J. / Jameson, G.B. / Jiao, W. / Hutton, R.H. / Webby, C.J. / Baker, E.N. / Baker, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Synergistic allostery, a sophisticated regulatory network for the control of aromatic amino acid biosynthesis in Mycobacterium tuberculosis Authors: Webby, C.J. / Jiao, W. / Hutton, R.D. / Blackmore, N.J. / Baker, H.M. / Baker, E.N. / Jameson, G.B. / Parker, E.J. #1: 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 | 3nv8.cif.gz | 321.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nv8.ent.gz | 253.7 KB | Display | PDB format |
PDBx/mmJSON format | 3nv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nv8_validation.pdf.gz | 492.6 KB | Display | wwPDB validaton report |
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Full document | 3nv8_full_validation.pdf.gz | 517.7 KB | Display | |
Data in XML | 3nv8_validation.xml.gz | 40 KB | Display | |
Data in CIF | 3nv8_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/3nv8 ftp://data.pdbj.org/pub/pdb/validation_reports/nv/3nv8 | HTTPS FTP |
-Related structure data
Related structure data | 3kgfSC 3nudC 3nueC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 6 / Auth seq-ID: 20 - 462 / Label seq-ID: 22 - 464
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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) / Strain: H37RV / Gene: RV2178C / Plasmid: PPROEXHTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase |
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-Non-polymers , 7 types, 294 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PEP / | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-PO4 / | #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: 3.91 Å3/Da / Density % sol: 68.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20MM BTP, 150MM NACL, 0.5MM TCEP, 0.2MM PEP, 0.1MM MNCL2, 0.1M HEPES, 0.8M NAK PHOSPHATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 11, 2009 / Details: AXCO PX70 |
Radiation | Monochromator: AXCO PX70 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→39.4 Å / Num. all: 73037 / Num. obs: 73037 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 6.11 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.4 / Num. unique all: 7137 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KGF (stripped of ligands and waters) Resolution: 2.25→39.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.262 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.158 / 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: 36.915 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→39.37 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5608 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.247→2.305 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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