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Yorodumi- PDB-3nud: The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nud | ||||||
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Title | The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with phenylalanine | ||||||
Components | Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG | ||||||
Keywords | TRANSFERASE / Mycobacterium tuberculosis / DAH7P synthase / Shikimate pathway / Aromatic biosynthesis / Evolutionary relationships / Phe-bound / Augmented TIM-barrel structure | ||||||
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: 3 Å | ||||||
Authors | Parker, E.J. / Jameson, G.B. / Jiao, W. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nud.cif.gz | 300.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nud.ent.gz | 239.3 KB | Display | PDB format |
PDBx/mmJSON format | 3nud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nud_validation.pdf.gz | 476.8 KB | Display | wwPDB validaton report |
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Full document | 3nud_full_validation.pdf.gz | 503.3 KB | Display | |
Data in XML | 3nud_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 3nud_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/3nud ftp://data.pdbj.org/pub/pdb/validation_reports/nu/3nud | HTTPS FTP |
-Related structure data
Related structure data | 3kgfC 3nueC 3nv8C 2b7oS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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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) / 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 #2: Chemical | ChemComp-PHE / #3: Chemical | ChemComp-PO4 / #4: 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: 3.96 Å3/Da / Density % sol: 68.95 % |
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Crystal grow | Temperature: 295 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 295K |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2005 / Details: OSMIC BLUE MIRRORS |
Radiation | Monochromator: OSMIC BLUE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 3→39.6 Å / Num. all: 31363 / Num. obs: 31363 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.63 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 3→3.077 Å / Redundancy: 2.68 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3 / Num. unique all: 31363 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B7O Resolution: 3→39.55 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.824 / SU B: 36.052 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.375 / ESU R Free: 0.405 / 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: 32.676 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→39.55 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3→3.077 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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