+Open data
-Basic information
Entry | Database: PDB / ID: 3dqz | ||||||
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Title | Structure of the hydroxynitrile lyase from Arabidopsis thaliana | ||||||
Components | Alpha-hydroxynitrile lyase-like protein | ||||||
Keywords | LYASE / A/B-Hydrloase fold / Cyanogenesis | ||||||
Function / homology | Function and homology information mandelonitrile lyase activity / (R)-mandelonitrile lyase / glycoside catabolic process / response to wounding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.504 Å | ||||||
Authors | Andexer, J. / Staunig, N. / Gruber, K. | ||||||
Citation | Journal: Chembiochem / Year: 2012 Title: Hydroxynitrile lyases with alpha / beta-hydrolase fold: two enzymes with almost identical 3D structures but opposite enantioselectivities and different reaction mechanisms Authors: Andexer, J.N. / Staunig, N. / Eggert, T. / Kratky, C. / Pohl, M. / Gruber, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dqz.cif.gz | 205.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dqz.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 3dqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/3dqz ftp://data.pdbj.org/pub/pdb/validation_reports/dq/3dqz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 29253.684 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F18D22_70, At5g10300 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LFT6 #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | |
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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: 2.36 Å3/Da / Density % sol: 47.86 % / Mosaicity: 0.834 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10-18% PEG3350, 100mM BisTris, pH6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8081 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8081 Å / Relative weight: 1 |
Reflection twin | Operator: l,-k,h / Fraction: 0.481 |
Reflection | Resolution: 2.5→30 Å / Num. all: 33151 / Num. obs: 33151 / % possible obs: 89.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.071 / Χ2: 1.076 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 2107 / Rsym value: 0.21 / Χ2: 0.939 / % possible all: 87.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QJ4, 1DWP, 1XKL Resolution: 2.504→24.171 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.862 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: This is a twinned structure, the detwin fraction is 0.481 and operator is 'l,-k,h'.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.792 Å2 / ksol: 0.352 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.9 Å2 / Biso mean: 27.936 Å2 / Biso min: 2.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.504→24.171 Å
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Refine LS restraints |
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