+Open data
-Basic information
Entry | Database: PDB / ID: 8wco | ||||||
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Title | (S)-citramalyl-CoA lyase | ||||||
Components | Probable acyl-CoA lyase beta chain | ||||||
Keywords | LYASE / (S)-citramalyl-CoA lyase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Huang, Q. / Bao, R. | ||||||
Funding support | 1items
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Citation | Journal: Structure / Year: 2024 Title: Structural and functional characterization of itaconyl-CoA hydratase and citramalyl-CoA lyase involved in itaconate metabolism of Pseudomonas aeruginosa. Authors: Huang, Q. / Duan, C. / Ma, H. / Nong, C. / Zheng, Q. / Zhou, J. / Zhao, N. / Mou, X. / Liu, T. / Zou, S. / Yang, N. / Tong, A. / Qin, W. / Bao, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wco.cif.gz | 366.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wco.ent.gz | 246.1 KB | Display | PDB format |
PDBx/mmJSON format | 8wco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wco_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8wco_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8wco_validation.xml.gz | 32 KB | Display | |
Data in CIF | 8wco_validation.cif.gz | 42.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/8wco ftp://data.pdbj.org/pub/pdb/validation_reports/wc/8wco | HTTPS FTP |
-Related structure data
Related structure data | 8khgC 8khlC 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 275 / Label seq-ID: 1 - 275
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-Components
#1: Protein | Mass: 29058.328 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA0883 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I562 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 52.44 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.25 M K2HPO4, 22% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.79 Å / Num. obs: 26786 / % possible obs: 97.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.02 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.6→2.67 Å / Num. unique obs: 3101 / CC1/2: 0.912 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.79 Å / SU ML: 0.384 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.3996 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→39.79 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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