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Yorodumi- PDB-2qhf: Mycobacterium tuberculosis Chorismate synthase in complex with NCA -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qhf | ||||||
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Title | Mycobacterium tuberculosis Chorismate synthase in complex with NCA | ||||||
Components | Chorismate synthase | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information chorismate synthase / chorismate synthase activity / Chorismate via Shikimate Pathway / oxidoreductase activity, acting on NAD(P)H / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NAD binding / FMN binding / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Bruning, M. / Bourenkov, G.P. / Strizhov, N.I. / Bartunik, H.D. | ||||||
Citation | Journal: To be Published Title: Mycobacterium tuberculosis Chorismate synthase in complex with NCA Authors: Bruning, M. / Bourenkov, G.P. / Strizhov, N.I. / Bartunik, H.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qhf.cif.gz | 103.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qhf.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 2qhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qhf_validation.pdf.gz | 459.7 KB | Display | wwPDB validaton report |
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Full document | 2qhf_full_validation.pdf.gz | 463.4 KB | Display | |
Data in XML | 2qhf_validation.xml.gz | 22 KB | Display | |
Data in CIF | 2qhf_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/2qhf ftp://data.pdbj.org/pub/pdb/validation_reports/qh/2qhf | HTTPS FTP |
-Related structure data
Related structure data | 1qxoS 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42673.250 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: aroC, aroF / Plasmid: pET24b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: P63611, UniProt: P9WPY1*PLUS, chorismate synthase |
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-Non-polymers , 6 types, 490 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-NCA / | #6: Chemical | ChemComp-TRS / | #7: 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: 4.84 Å3/Da / Density % sol: 74.57 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 4.8 M NH4-Acetate, 0.1 M Na-Acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. obs: 98095 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 1.65→1.67 Å / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3904 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QXO Resolution: 1.65→19.65 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.203 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.059 / ESU R Free: 0.062 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.497 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→19.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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