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Yorodumi- PDB-5z9a: Crystal structure of chorismate synthase from Pseudomonas aeruginosa -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z9a | ||||||
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Title | Crystal structure of chorismate synthase from Pseudomonas aeruginosa | ||||||
Components | Chorismate synthase | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information chorismate synthase / chorismate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Iqbal, N. / Chaudhary, A. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of chorismate synthase from Pseudomonas aeruginosa Authors: Iqbal, N. / Chaudhary, 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 | 5z9a.cif.gz | 198.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z9a.ent.gz | 159.2 KB | Display | PDB format |
PDBx/mmJSON format | 5z9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/5z9a ftp://data.pdbj.org/pub/pdb/validation_reports/z9/5z9a | HTTPS FTP |
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-Related structure data
Related structure data | 1r53S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 1 - 349 / Label seq-ID: 1 - 349
NCS oper:
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-Components
#1: Protein | Mass: 39036.066 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain LESB58) (bacteria) Strain: LESB58 / Gene: aroC, PLES_36461 / Production host: Escherichia coli (E. coli) / References: UniProt: B7UV40, chorismate synthase #2: 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: 2.11 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 10mM HEPES pH 7.5, 8% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→66.28 Å / Num. obs: 17307 / % possible obs: 96.36 % / Redundancy: 5.92 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 11.05 |
Reflection shell | Resolution: 2.791→2.891 Å / Rmerge(I) obs: 0.43 / Num. measured obs: 7302 / Num. unique obs: 887 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R53 Resolution: 2.79→66.28 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 34.162 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.898 / ESU R Free: 0.377 / 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: 96.169 Å2
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Refinement step | Cycle: 1 / Resolution: 2.79→66.28 Å
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Refine LS restraints |
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