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- PDB-5kvb: The crystal structure of hexachlorocyclohexane dehydrochlorinase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kvb | ||||||
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Title | The crystal structure of hexachlorocyclohexane dehydrochlorinase LinA-type3 from Novosphingobium barchaimii LL02 | ||||||
![]() | Gamma-hexachlorocyclohexane dehydrochlorinase | ||||||
![]() | LYASE / dehydrochlorinase | ||||||
Function / homology | SnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Gamma-hexachlorocyclohexane dehydrochlorinase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dellas, N. / Oakeshott, J. / Pearce, S.L. / Pandey, G. / Pushiri, H. | ||||||
![]() | ![]() Title: The crystal structure of hexachlorocyclohexane dehydrochlorinase LinA-type3 from Novosphingobium barchaimii LL02 Authors: Dellas, N. / Oakeshott, J. / Pearce, S.L. / Pandey, G. / Pushiri, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.9 KB | Display | ![]() |
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PDB format | ![]() | 31.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 405.7 KB | Display | ![]() |
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Full document | ![]() | 406.3 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a76S S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 17720.896 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: DSMZ 25411 Source: (gene. exp.) ![]() Gene: V474_07160 / Plasmid: pDEST14 / Details (production host): gateway / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.05 Details: 20.5% PEG 1000, 10% propionate-cacodylate-bis tris propane |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 7, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→41.688 Å / Num. all: 24639 / Num. obs: 24639 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 10.68 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.057 / Rsym value: 0.052 / Net I/av σ(I): 9.804 / Net I/σ(I): 19.6 / Num. measured all: 140021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A76 Resolution: 1.45→37.465 Å / Cross valid method: FREE R-VALUE / σ(F): 1.99 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.36 Å2 / Biso mean: 13.211 Å2 / Biso min: 3.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→37.465 Å
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Refine LS restraints |
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LS refinement shell |
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