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- PDB-6r76: Crystal structure of trans-3-Hydroxy-L-proline dehydratase from T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r76 | ||||||
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Title | Crystal structure of trans-3-Hydroxy-L-proline dehydratase from Thermococcus litoralis - open conformation | ||||||
![]() | (Proline racemase) x 2 | ||||||
![]() | LYASE / Hydro-lyase / hydroxyproline dehydratase | ||||||
Function / homology | Proline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / Proline racemase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferraris, D.M. / Miggiano, R. / Rizzi, M. | ||||||
![]() | ![]() Title: Structure of Thermococcus litoralis trans-3-hydroxy-l-proline dehydratase in the free and substrate-complexed form. Authors: Ferraris, D.M. / Miggiano, R. / Watanabe, S. / Rizzi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 274.7 KB | Display | ![]() |
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PDB format | ![]() | 222.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.1 KB | Display | ![]() |
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Full document | ![]() | 491.7 KB | Display | |
Data in XML | ![]() | 48.6 KB | Display | |
Data in CIF | ![]() | 66.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r77C ![]() 1w61S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41675.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The construct carries an N-term 6xHis-tag and a TEV cleavage site Source: (gene. exp.) ![]() ![]() Gene: OCC_00387 / Variant: ATCC 51850 / DSM 5473 / JCM 8560 / NS-C / Production host: ![]() ![]() #2: Protein | Mass: 41755.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The construct carries an N-term 6xHis-tag and a TEV cleavage site Source: (gene. exp.) ![]() ![]() Gene: OCC_00387 / Variant: ATCC 51850 / DSM 5473 / JCM 8560 / NS-C / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Magnesium formate, 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979163 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→44.8 Å / Num. obs: 53298 / % possible obs: 99.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 0.41 / Num. unique obs: 5281 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1W61 Resolution: 2.4→44.8 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→44.8 Å
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Refine LS restraints |
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LS refinement shell |
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