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Yorodumi- PDB-5gxd: Structure of acryloyl-CoA lyase PrpE from Dinoroseobacter shibae ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gxd | ||||||
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Title | Structure of acryloyl-CoA lyase PrpE from Dinoroseobacter shibae DFL 12 | ||||||
Components | AMP-dependent synthetase and ligase | ||||||
Keywords | LYASE / acryloyl-CoA / acrylate | ||||||
Function / homology | Function and homology information Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / ligase activity Similarity search - Function | ||||||
Biological species | Dinoroseobacter shibae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Zhang, Y.Z. / Wang, P. / Cao, H.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of acryloyl-CoA lyase PrpE from Dinoroseobacter shibae DFL 12 Authors: Zhang, Y.Z. / Wang, P. / Cao, H.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gxd.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gxd.ent.gz | 113.5 KB | Display | PDB format |
PDBx/mmJSON format | 5gxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gxd_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5gxd_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5gxd_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 5gxd_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/5gxd ftp://data.pdbj.org/pub/pdb/validation_reports/gx/5gxd | HTTPS FTP |
-Related structure data
Related structure data | 2p2bS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 68485.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12) (bacteria) Strain: DSM 16493 / NCIMB 14021 / DFL 12 / Gene: Dshi_0825 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A8LRC0, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases |
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-Non-polymers , 5 types, 544 molecules
#2: Chemical | ChemComp-AMP / | ||
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#3: Chemical | ChemComp-AKR / | ||
#4: Chemical | ChemComp-COA / | ||
#5: Chemical | ChemComp-GOL / #6: 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: 2.79 Å3/Da / Density % sol: 55.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.8M Ammonium sulfate, 0.1M BIS-TRIS pH 6.5, 2% polyethylene glycol(PEG) monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.0008→50 Å / Num. obs: 50809 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 28.07 |
Reflection shell | Resolution: 2.001→2.073 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.287 / Num. unique obs: 4985 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2P2B Resolution: 2.001→31.316 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.79 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→31.316 Å
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Refine LS restraints |
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LS refinement shell |
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