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Yorodumi- PDB-6vxc: Crystal structure of hydroxyproline dehydratase (HypD) from Clost... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vxc | |||||||||
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Title | Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile | |||||||||
Components | Trans-4-hydroxy-L-proline dehydratase | |||||||||
Keywords | LYASE / glycyl radical enzyme / hydroxyproline dehydratase | |||||||||
Function / homology | Function and homology information trans-4-hydroxy-L-proline dehydratase / proline salvage / formate C-acetyltransferase / formate C-acetyltransferase activity / carbon-oxygen lyase activity / lyase activity Similarity search - Function | |||||||||
Biological species | Clostridioides difficile 70-100-2010 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Backman, L.R.F. / Drennan, C.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Elife / Year: 2020 Title: Molecular basis for catabolism of the abundant metabolitetrans-4-hydroxy-L-proline by a microbial glycyl radical enzyme. Authors: Backman, L.R. / Huang, Y.Y. / Andorfer, M.C. / Gold, B. / Raines, R.T. / Balskus, E.P. / Drennan, C.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vxc.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6vxc.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6vxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vxc_validation.pdf.gz | 277.7 KB | Display | wwPDB validaton report |
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Full document | 6vxc_full_validation.pdf.gz | 277.5 KB | Display | |
Data in XML | 6vxc_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 6vxc_validation.cif.gz | 81.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/6vxc ftp://data.pdbj.org/pub/pdb/validation_reports/vx/6vxc | HTTPS FTP |
-Related structure data
Related structure data | 6vxeC 5fauS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 91456.609 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile 70-100-2010 (bacteria) Gene: pflD, csdB_2, BGU81_07860, BN1095_640054, BN1096_740112, BN1097_360077, SAMEA3375004_02654 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A031WDE4, UniProt: Q180C6*PLUS, trans-4-hydroxy-L-proline dehydratase #2: Chemical | ChemComp-GOL / #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: 2.74 Å3/Da / Density % sol: 55.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14% (w/v) polyethylene glycol (PEG) 3350, 100 mM potassium chloride, and 100 mM HEPES pH 7.5. Cryoprotectant contained 15% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.048→50 Å / Num. obs: 486251 / % possible obs: 99 % / Redundancy: 7.07 % / CC1/2: 0.99 / Rsym value: 0.168 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 7.01 % / Mean I/σ(I) obs: 1.82 / Num. unique obs: 24062 / CC1/2: 0.588 / Rsym value: 0.757 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FAU Resolution: 2.05→49.817 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.55 Å2 / Biso mean: 21.0358 Å2 / Biso min: 6.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.05→49.817 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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