+Open data
-Basic information
Entry | Database: PDB / ID: 8gqn | ||||||
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Title | X-ray structure of thiolase with CoA | ||||||
Components | Thiolase | ||||||
Keywords | TRANSFERASE / acetyl-CoA acetyltransferase thiolase | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Hong, J. / Son, H.F. / Kim, K.J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of thiolase from Pseudomonas aeruginosa PAO1 Authors: Hong, J. / Son, H.F. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gqn.cif.gz | 289 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gqn.ent.gz | 234.7 KB | Display | PDB format |
PDBx/mmJSON format | 8gqn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gqn_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8gqn_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8gqn_validation.xml.gz | 56 KB | Display | |
Data in CIF | 8gqn_validation.cif.gz | 75.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/8gqn ftp://data.pdbj.org/pub/pdb/validation_reports/gq/8gqn | HTTPS FTP |
-Related structure data
Related structure data | 8gqfC 8gqgC 8gqhC 8gqiC 8gqjC 8gqkC 8gqlC 8gqmC 4n44S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41669.664 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA3925 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G3XD40 #2: Chemical | ChemComp-COA / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.25 Å3/Da / Density % sol: 45.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG 3350 200 mM Magnesium formate dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 6, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 39810 / % possible obs: 97.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.092 / Rrim(I) all: 0.178 / Χ2: 5.386 / Net I/σ(I): 9.4 / Num. measured all: 124439 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N44 Resolution: 2.7→34.38 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.819 / SU B: 20.091 / SU ML: 0.393 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.459 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 103.03 Å2 / Biso mean: 37.762 Å2 / Biso min: 6.25 Å2
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Refinement step | Cycle: final / Resolution: 2.7→34.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.765 Å / Rfactor Rfree error: 0
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