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- PDB-6y9f: Crystal structure of putative ancestral haloalkane dehalogenase A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y9f | ||||||
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Title | Crystal structure of putative ancestral haloalkane dehalogenase AncHLD3 (node 3) | ||||||
![]() | Ancestral haloalkane dehalogenase AncHLD3 | ||||||
![]() | HYDROLASE / Haloalkane dehalogenase | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Chaloupkova, R. / Damborsky, J. / Marek, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics. Authors: Babkova, P. / Dunajova, Z. / Chaloupkova, R. / Damborsky, J. / Bednar, D. / Marek, 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 | ![]() | 142.5 KB | Display | ![]() |
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PDB format | ![]() | 110.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.6 KB | Display | ![]() |
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Full document | ![]() | 436 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y9eC ![]() 6y9gC ![]() 4k2aS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 34073.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: Sodium citrate tribasic, CHES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→61.852 Å / Num. obs: 92642 / % possible obs: 99.8 % / Redundancy: 17 % / CC1/2: 1 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.26→1.29 Å / Num. unique obs: 6558 / CC1/2: 0.564 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4K2A Resolution: 1.26→61.852 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.59 / 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: 113.35 Å2 / Biso mean: 24.7953 Å2 / Biso min: 11.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.26→61.852 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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