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- PDB-5e46: Hydroxynitrile lyase from the fern Davallia tyermanii -

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Basic information

Entry
Database: PDB / ID: 5.0E+46
TitleHydroxynitrile lyase from the fern Davallia tyermanii
ComponentsHydroxynitrile lyase
KeywordsLYASE / hydroxynitrile lyase / fern
Function / homology: / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / lyase activity / 2-Layer Sandwich / Alpha Beta / Hydroxynitrile lyase
Function and homology information
Biological speciesDavallia tyermannii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.854 Å
AuthorsPavkov-Keller, T. / Diepold, M. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austria
CitationJournal: Sci Rep / Year: 2017
Title: Enzyme discovery beyond homology: a unique hydroxynitrile lyase in the Bet v1 superfamily.
Authors: Lanfranchi, E. / Pavkov-Keller, T. / Koehler, E.M. / Diepold, M. / Steiner, K. / Darnhofer, B. / Hartler, J. / Van Den Bergh, T. / Joosten, H.J. / Gruber-Khadjawi, M. / Thallinger, G.G. / ...Authors: Lanfranchi, E. / Pavkov-Keller, T. / Koehler, E.M. / Diepold, M. / Steiner, K. / Darnhofer, B. / Hartler, J. / Van Den Bergh, T. / Joosten, H.J. / Gruber-Khadjawi, M. / Thallinger, G.G. / Birner-Gruenberger, R. / Gruber, K. / Winkler, M. / Glieder, A.
History
DepositionOct 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 1.2Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxynitrile lyase
B: Hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)47,0832
Polymers47,0832
Non-polymers00
Water8,413467
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-17 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.633, 94.020, 117.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Hydroxynitrile lyase


Mass: 23541.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GenBank asseccion number KT804569 / Source: (gene. exp.) Davallia tyermannii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C9V3S9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Native crystals of DtHNL1 were obtained by mixing 0.5ul 4 mg/mL protein sample (in 10 mM Tris-HCl pH 8.0) with 1 ul reservoir solution (0.9 M NaNO3; Na2HPO4; (NH4)2SO4 mix, 0.1 M Tris-Bicine ...Details: Native crystals of DtHNL1 were obtained by mixing 0.5ul 4 mg/mL protein sample (in 10 mM Tris-HCl pH 8.0) with 1 ul reservoir solution (0.9 M NaNO3; Na2HPO4; (NH4)2SO4 mix, 0.1 M Tris-Bicine Buffer pH 8.5 and 30% (w/v) polyethylene glycol monomethyl ether 550 & polyethylene glycol 20k; Morpheus condition C9). Additionally, native crystals were also grown by mixing 1 ul 4 mg/mL protein sample (in 10 mM Tris-HCl pH 8.0) with 0.5ul reservoir solution (0.1 M 2-(4-(2-hydroxyethyl)-1-piperazinyl) ethanesulfonic acid pH 7.5 and 10% (w/v) polyethylene glycol; JSCG condition B4). SeMet-DtHNL1 crystals were obtained in 0.2 M sodium thiocyanate, 20% (w/v) polyethylene glycol 3350. A 1:1 ratio of protein and screening solutions was used, using protein concentration of 3 mg/mL (in 10 mM Tris-HCl pH 8.0).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→58 Å / Num. obs: 34750 / % possible obs: 99.84 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.188 / Net I/σ(I): 9.97
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 13 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 2.57 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.854→57.971 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 1738 5 %
Rwork0.1548 --
obs0.1567 34748 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.854→57.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2749 0 0 467 3216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073021
X-RAY DIFFRACTIONf_angle_d1.0214143
X-RAY DIFFRACTIONf_dihedral_angle_d12.571074
X-RAY DIFFRACTIONf_chiral_restr0.046461
X-RAY DIFFRACTIONf_plane_restr0.005534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8543-1.90890.28661400.21452656X-RAY DIFFRACTION98
1.9089-1.97050.20591430.18652715X-RAY DIFFRACTION100
1.9705-2.0410.23441450.17672751X-RAY DIFFRACTION100
2.041-2.12270.18121420.16442703X-RAY DIFFRACTION100
2.1227-2.21930.21461440.15932730X-RAY DIFFRACTION100
2.2193-2.33630.22641440.15192736X-RAY DIFFRACTION100
2.3363-2.48270.19661430.1622736X-RAY DIFFRACTION100
2.4827-2.67440.19431450.1662745X-RAY DIFFRACTION100
2.6744-2.94350.21621450.1662752X-RAY DIFFRACTION100
2.9435-3.36940.19161470.15132787X-RAY DIFFRACTION100
3.3694-4.24490.16281460.12752785X-RAY DIFFRACTION100
4.2449-57.99910.15811540.14592914X-RAY DIFFRACTION100

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