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Yorodumi- PDB-7bpo: Hydroxynitrile lyase from Parafonteria laminate complexed with be... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bpo | |||||||||
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Title | Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde | |||||||||
Components | Hydroxynitrile lyase | |||||||||
Keywords | LYASE / hydroxynitrile lyase / millipede | |||||||||
Function / homology | benzaldehyde Function and homology information | |||||||||
Biological species | Parafontaria falcifera (arthropod) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.37 Å | |||||||||
Authors | Nuylert, A. / Nakabayashi, M. / Yamaguchi, T. / Asano, Y. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: To Be Published Title: Hydroxynitrile lyase from Parafonteria laminate complexed with benzaldehyde Authors: Nuylert, A. / Nakabayashi, M. / Yamaguchi, T. / Asano, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bpo.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bpo.ent.gz | 65.3 KB | Display | PDB format |
PDBx/mmJSON format | 7bpo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bpo_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7bpo_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7bpo_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 7bpo_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/7bpo ftp://data.pdbj.org/pub/pdb/validation_reports/bp/7bpo | HTTPS FTP |
-Related structure data
Related structure data | 6jhcS S: Starting model for refinement |
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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: 18180.303 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Parafontaria falcifera (arthropod) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffleT7 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: potassium thiocyanate, sodium acetate PEG 8000 and PEG 1000, benzaldehyde |
-Data collection
Diffraction | Mean temperature: 100 K / 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 6M / Detector: PIXEL / Date: May 29, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.37→69.168 Å / Num. all: 63260 / Num. obs: 63260 / % possible obs: 96.3 % / Redundancy: 6.6 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Rsym value: 0.082 / Net I/av σ(I): 4.1 / Net I/σ(I): 11.7 / Num. measured all: 420603 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JHC Resolution: 1.37→34.88 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.63 / SU ML: 0.027 / SU R Cruickshank DPI: 0.0565 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.056 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: 50.32 Å2 / Biso mean: 17.066 Å2 / Biso min: 9.69 Å2
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Refinement step | Cycle: final / Resolution: 1.37→34.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.37→1.406 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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