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Yorodumi- PDB-3uy4: Crystal Structure of Pantoate--Beta-Alanine Ligase from Campyloba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uy4 | ||||||
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Title | Crystal Structure of Pantoate--Beta-Alanine Ligase from Campylobacter jejuni complexed with AMP and vitamin B5 | ||||||
Components | Pantothenate synthetase | ||||||
Keywords | LIGASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta-alpha structure / cytosol | ||||||
Function / homology | Function and homology information pantoate-beta-alanine ligase (AMP-forming) / pantoate-beta-alanine ligase activity / pantothenate biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Campylobacter jejuni subsp. jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.851 Å | ||||||
Authors | Kim, Y. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Pantoate--Beta-Alanine Ligase from Campylobacter jejuni complexed with AMP and vitamin B5 Authors: Kim, Y. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uy4.cif.gz | 131.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uy4.ent.gz | 108.7 KB | Display | PDB format |
PDBx/mmJSON format | 3uy4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/3uy4 ftp://data.pdbj.org/pub/pdb/validation_reports/uy/3uy4 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-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
#1: Protein | Mass: 32917.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter) Strain: NCTC 11168 / Gene: Cj0297c, panC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic References: UniProt: Q9PIK2, pantoate-beta-alanine ligase (AMP-forming) |
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#2: Chemical | ChemComp-AMP / |
#3: Chemical | ChemComp-PAU / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.29 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 %(w/v) PEG8000, HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2011 / Details: mirrors |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 26959 / Num. obs: 26959 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 21.94 Å2 / Rsym value: 0.068 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1277 / Rsym value: 0.771 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.851→40.18 Å / SU ML: 0.39 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.94 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.63 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.851→40.18 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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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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