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- PDB-7br1: Hydroxynitrile lyase from Parafontaria laminate complexed with be... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7br1 | |||||||||
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Title | Hydroxynitrile lyase from Parafontaria laminate complexed with benzaldehyde prepared by cocrystallization | |||||||||
![]() | Hydroxynitrile lyase | |||||||||
![]() | LYASE / hydroxynitrile lyase / millipede | |||||||||
Function / homology | benzaldehyde / THIOCYANATE ION![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Nuylert, A. / Nakabayashi, M. / Yamaguchi, T. / Asano, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde prepared by cocrystallization Authors: Nuylert, A. / Nakabayashi, M. / Yamaguchi, T. / Asano, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.9 KB | Display | ![]() |
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PDB format | ![]() | 66.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jhcS 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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Unit cell |
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Components
#1: Protein | Mass: 18123.248 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parafontaria laminata / Production host: ![]() ![]() #2: Chemical | ChemComp-HBX / #3: Chemical | ChemComp-SCN / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: potassium thiocyanate, sodium acetate pH 5.5, 10% w/v PEG 8000, 10% w/v PEG 1000, benzaldehyde |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→82.517 Å / Num. all: 84891 / Num. obs: 84891 / % possible obs: 100 % / Redundancy: 6.6 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Rsym value: 0.053 / Net I/av σ(I): 10.5 / Net I/σ(I): 18.1 / Num. measured all: 556553 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JHC Resolution: 1.25→41.98 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.409 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0381 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.037 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.7 Å2 / Biso mean: 13.322 Å2 / Biso min: 8.03 Å2
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Refinement step | Cycle: final / Resolution: 1.25→41.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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