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Yorodumi- PDB-4o90: Crystal structure of chorismate synthase from Acinetobacter bauma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o90 | ||||||
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Title | Crystal structure of chorismate synthase from Acinetobacter baumannii at 2.6A resolution | ||||||
Components | Chorismate synthase | ||||||
Keywords | LYASE / synthesis of chorismate | ||||||
Function / homology | Function and homology information chorismate synthase / chorismate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / FMN binding / cytosol Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Chaudhary, A. / Singh, N. / Shukla, P.K. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To be Published Title: Crystal structure of chorismate synthase from Acinetobacter baumannii at 2.6A resolution Authors: Chaudhary, A. / Singh, N. / Shukla, P.K. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o90.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o90.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 4o90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o90_validation.pdf.gz | 467 KB | Display | wwPDB validaton report |
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Full document | 4o90_full_validation.pdf.gz | 490.1 KB | Display | |
Data in XML | 4o90_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 4o90_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/4o90 ftp://data.pdbj.org/pub/pdb/validation_reports/o9/4o90 | HTTPS FTP |
-Related structure data
Related structure data | 4lj2S 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: 39051.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ATCC 19606 / Gene: aroC / Production host: Escherichia coli (E. coli) / References: UniProt: D0C7F3, chorismate synthase #2: Chemical | #3: Chemical | #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: 2.3 Å3/Da / Density % sol: 46.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50mM Tris-HCl, 0.2M MgCl2, 20% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 10, 2013 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→32.37 Å / Num. all: 22516 / Num. obs: 21001 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 55.6 Å2 |
Reflection shell | Resolution: 2.6→2.7 Å / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LJ2 Resolution: 2.61→32.37 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2664768.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.0621 Å2 / ksol: 0.267843 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.61→32.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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