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- PDB-5e4b: Hydroxynitrile lyase from the fern Davallia tyermanii in complex ... -

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Basic information

Entry
Database: PDB / ID: 5e4b
TitleHydroxynitrile lyase from the fern Davallia tyermanii in complex with (R)-mandelonitrile / benzaldehyde
ComponentsHydroxynitrile lyase
KeywordsLYASE / hydroxynitrile lyase / fern / (R)-mandelonitrile / benzaldehyde
Function / homology
Function and homology information


: / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
benzaldehyde / (2R)-hydroxy(phenyl)ethanenitrile / Hydroxynitrile lyase
Similarity search - Component
Biological speciesDavallia tyermannii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 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 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9986
Polymers46,5202
Non-polymers4794
Water9,728540
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-17 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.362, 94.135, 116.143
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: 23259.975 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: Chemical ChemComp-HBX / benzaldehyde


Mass: 106.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O
#3: Chemical ChemComp-MXN / (2R)-hydroxy(phenyl)ethanenitrile / (R)-mandelonitrile


Mass: 133.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
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).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.5→35.8 Å / Num. obs: 63070 / % possible obs: 97.48 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.74
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.86 / % possible all: 80.88

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5.0E+46 / Resolution: 1.5→35.8 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 3154 5 %
Rwork0.1562 --
obs0.1573 63062 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 36 540 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073050
X-RAY DIFFRACTIONf_angle_d1.0334177
X-RAY DIFFRACTIONf_dihedral_angle_d12.5141075
X-RAY DIFFRACTIONf_chiral_restr0.047461
X-RAY DIFFRACTIONf_plane_restr0.005538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4988-1.52110.31030.29061965X-RAY DIFFRACTION75
1.5211-1.54490.2811200.26182262X-RAY DIFFRACTION85
1.5449-1.57020.24081270.23912411X-RAY DIFFRACTION91
1.5702-1.59730.2391310.22282499X-RAY DIFFRACTION95
1.5973-1.62640.20791380.2012619X-RAY DIFFRACTION100
1.6264-1.65760.20641390.19252638X-RAY DIFFRACTION100
1.6576-1.69150.22861390.1922635X-RAY DIFFRACTION100
1.6915-1.72830.23991400.18912663X-RAY DIFFRACTION100
1.7283-1.76850.22171390.18662637X-RAY DIFFRACTION100
1.7685-1.81270.20631390.17922654X-RAY DIFFRACTION100
1.8127-1.86170.20051390.17042631X-RAY DIFFRACTION100
1.8617-1.91650.21291400.1592654X-RAY DIFFRACTION100
1.9165-1.97830.18381410.15222686X-RAY DIFFRACTION100
1.9783-2.0490.16021390.15122641X-RAY DIFFRACTION100
2.049-2.1310.18741400.14812663X-RAY DIFFRACTION100
2.131-2.2280.16241410.14252670X-RAY DIFFRACTION100
2.228-2.34550.17571390.14742656X-RAY DIFFRACTION100
2.3455-2.49240.16371420.15422694X-RAY DIFFRACTION100
2.4924-2.68480.17681410.15192686X-RAY DIFFRACTION100
2.6848-2.95480.16111420.15842682X-RAY DIFFRACTION100
2.9548-3.38210.17961410.14482690X-RAY DIFFRACTION100
3.3821-4.260.14581440.12812734X-RAY DIFFRACTION100
4.26-35.81480.15841500.13572838X-RAY DIFFRACTION99

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