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Yorodumi- PDB-6kfc: Hydroxynitrile lyase from the millipede, Chamberlinius hualienens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kfc | |||||||||
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Title | Hydroxynitrile lyase from the millipede, Chamberlinius hualienensis, complexed with cyanide ion | |||||||||
Components | Hydroxynitrile lyase | |||||||||
Keywords | LYASE / Hydroxynitrile lyase / lipocalin fold / four disulfide bonds / dimer | |||||||||
Function / homology | Ricin B-like lectins / lyase activity / CYANIDE ION / Hydroxynitrile lyase Function and homology information | |||||||||
Biological species | Chamberlinius hualienensis (arthropod) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Motojima, F. / Izumi, A. / Asano, Y. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: Febs J. / Year: 2021 Title: R-hydroxynitrile lyase from the cyanogenic millipede, Chamberlinius hualienensis-A new entry to the carrier protein family Lipocalines. Authors: Motojima, F. / Izumi, A. / Nuylert, A. / Zhai, Z. / Dadashipour, M. / Shichida, S. / Yamaguchi, T. / Nakano, S. / Asano, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kfc.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kfc.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 6kfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kfc_validation.pdf.gz | 725.1 KB | Display | wwPDB validaton report |
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Full document | 6kfc_full_validation.pdf.gz | 725.5 KB | Display | |
Data in XML | 6kfc_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 6kfc_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/6kfc ftp://data.pdbj.org/pub/pdb/validation_reports/kf/6kfc | HTTPS FTP |
-Related structure data
Related structure data | 6jhcC 6kfaSC 6kfbC 6kfdC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18241.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chamberlinius hualienensis (arthropod) / References: UniProt: A0A0H5BR52 |
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#2: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CYN / |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.83 % / Description: bipyramid |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate (pH 5.0), 28-32% (w/v) PEG monomethyl ether 2000, 0.3 M NDSB-195 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: N2 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 20, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50.74 Å / Num. obs: 14405 / % possible obs: 100 % / Redundancy: 19.5 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.037 / Rrim(I) all: 0.122 / Rsym value: 0.116 / Net I/av σ(I): 19.3 / Net I/σ(I): 3 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 20.5 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 2022 / CC1/2: 0.971 / Rpim(I) all: 0.187 / Rrim(I) all: 0.627 / Rsym value: 0.598 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KFA Resolution: 2.1→50.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.051 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 32.195 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→50.74 Å
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