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Yorodumi- PDB-5xzd: Structure of acryloyl-CoA hydratase AcuH from Roseovarius nubinhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xzd | |||||||||||||||
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Title | Structure of acryloyl-CoA hydratase AcuH from Roseovarius nubinhibens ISM | |||||||||||||||
Components | Enoyl-CoA hydratase | |||||||||||||||
Keywords | LYASE / acryloyl-CoA / hydratase / acrylate | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Roseovarius nubinhibens (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||||||||
Authors | Zhang, Y.Z. / Wang, P. / Cao, H.Y. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Front Microbiol / Year: 2017 Title: Molecular Insight into the Acryloyl-CoA Hydration by AcuH for Acrylate Detoxification in Dimethylsulfoniopropionate-Catabolizing Bacteria Authors: Cao, H.Y. / Wang, P. / Xu, F. / Li, P.Y. / Xie, B.B. / Qin, Q.L. / Zhang, Y.Z. / Li, C.Y. / Chen, X.L. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xzd.cif.gz | 280.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xzd.ent.gz | 225.2 KB | Display | PDB format |
PDBx/mmJSON format | 5xzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xzd_validation.pdf.gz | 481.6 KB | Display | wwPDB validaton report |
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Full document | 5xzd_full_validation.pdf.gz | 491.8 KB | Display | |
Data in XML | 5xzd_validation.xml.gz | 56 KB | Display | |
Data in CIF | 5xzd_validation.cif.gz | 79.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/5xzd ftp://data.pdbj.org/pub/pdb/validation_reports/xz/5xzd | HTTPS FTP |
-Related structure data
Related structure data | 3h81S 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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-Components
#1: Protein | Mass: 28327.758 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: The densities of residues 236-258 are missing. Source: (gene. exp.) Roseovarius nubinhibens (strain ATCC BAA-591 / DSM 15170 / ISM) (bacteria) Strain: ATCC BAA-591 / DSM 15170 / ISM / Gene: ISM_05820 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A3SKA6 #2: Chemical | ChemComp-ACY / #3: 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: 2.63 Å3/Da / Density % sol: 53.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M sodium acetate (pH 5.2), 15% (v/v) 2-methyl-1,3-propanediol and 2.2% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 137287 / % possible obs: 99.34 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 41.37 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 3.5 % / Num. unique obs: 13424 / % possible all: 97.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H81 Resolution: 1.9→48.381 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.381 Å
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Refine LS restraints |
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LS refinement shell |
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