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Yorodumi- PDB-2y27: crystal structure of PaaK1 in complex with ATP from Burkholderia ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y27 | ||||||
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Title | crystal structure of PaaK1 in complex with ATP from Burkholderia cenocepacia | ||||||
Components | PHENYLACETATE-COENZYME A LIGASE | ||||||
Keywords | LIGASE / PHENYLACETIC ACID DEGRADATION PATHWAY | ||||||
Function / homology | Function and homology information phenylacetate-CoA ligase / phenylacetate-CoA ligase activity / phenylacetate catabolic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | BURKHOLDERIA CENOCEPACIA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Law, A. / Boulanger, M.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Defining a Structural and Kinetic Rationale for Paralogous Copies of Phenylacetate-Coa Ligases from the Cystic Fibrosis Pathogen Burkholderia Cenocepacia J2315. Authors: Law, A. / Boulanger, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y27.cif.gz | 203.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y27.ent.gz | 167.5 KB | Display | PDB format |
PDBx/mmJSON format | 2y27.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y27_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2y27_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2y27_validation.xml.gz | 44 KB | Display | |
Data in CIF | 2y27_validation.cif.gz | 66.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y2/2y27 ftp://data.pdbj.org/pub/pdb/validation_reports/y2/2y27 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 48709.648 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: J2315 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4E7B5, phenylacetate-CoA ligase |
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-Non-polymers , 7 types, 976 molecules
#2: Chemical | ChemComp-SCN / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-BME / #5: Chemical | ChemComp-PG4 / | #6: Chemical | #7: Chemical | ChemComp-MG / #8: 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: 2.59 Å3/Da / Density % sol: 52.58 % / Description: NONE |
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Crystal grow | Details: 2% PEG 3350, 200 MM KSCN, 5% GLYCEROL. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9792 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 121839 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.6→29.98 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.705 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.083 / 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: 21.869 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.98 Å
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