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- PDB-3dqz: Structure of the hydroxynitrile lyase from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 3dqz
TitleStructure of the hydroxynitrile lyase from Arabidopsis thaliana
ComponentsAlpha-hydroxynitrile lyase-like protein
KeywordsLYASE / 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
Methylesterase/Alpha-hydroxynitrile lyase / Alpha/beta hydrolase family / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-hydroxynitrile lyase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.504 Å
AuthorsAndexer, J. / Staunig, N. / Gruber, K.
CitationJournal: 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
DepositionJul 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 14, 2012Group: Other
Revision 1.3Apr 25, 2012Group: Other
Revision 1.4Oct 23, 2013Group: Database references
Revision 1.5Oct 25, 2017Group: Refinement description / Category: software
Revision 1.6Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-hydroxynitrile lyase-like protein
B: Alpha-hydroxynitrile lyase-like protein
C: Alpha-hydroxynitrile lyase-like protein
D: Alpha-hydroxynitrile lyase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,0505
Polymers117,0154
Non-polymers351
Water1,24369
1
A: Alpha-hydroxynitrile lyase-like protein
B: Alpha-hydroxynitrile lyase-like protein


Theoretical massNumber of molelcules
Total (without water)58,5072
Polymers58,5072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alpha-hydroxynitrile lyase-like protein
D: Alpha-hydroxynitrile lyase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5433
Polymers58,5072
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.248, 223.313, 50.201
Angle α, β, γ (deg.)90.000, 101.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.892166, -0.224244, -0.392115), (-0.243977, -0.491335, 0.836101), (-0.380151, 0.841608, 0.383642)-12.0917, 6.46592, -7.37886
2given(0.194955, -0.002658, -0.980809), (-0.005533, -0.999983, 0.001611), (-0.980797, 0.005113, -0.194967)-16.274, -56.475101, -27.6068
3given(0.203611, 0.223737, 0.953144), (-0.86917, 0.489421, 0.070787), (-0.450651, -0.842857, 0.294117)25.7353, 14.5475, -59.554901

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Components

#1: Protein
Alpha-hydroxynitrile lyase-like protein / AtHNL / AT5g10300/F18D22_70


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 / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.86 % / Mosaicity: 0.834 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10-18% PEG3350, 100mM BisTris, pH6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8081 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8081 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.481
ReflectionResolution: 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 shellResolution: 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

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJ4, 1DWP, 1XKL

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'.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1561 4.72 %random
Rwork0.159 ---
obs-33106 89.34 %-
Solvent computationShrinkage 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 parametersBiso max: 86.9 Å2 / Biso mean: 27.936 Å2 / Biso min: 2.78 Å2
Baniso -1Baniso -2Baniso -3
1--1.179 Å2-0 Å2-2.062 Å2
2--1.958 Å2-0 Å2
3----0.779 Å2
Refinement stepCycle: LAST / Resolution: 2.504→24.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8130 0 1 69 8200
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.8991
X-RAY DIFFRACTIONf_bond_d0.0061
X-RAY DIFFRACTIONf_chiral_restr0.0631
X-RAY DIFFRACTIONf_dihedral_angle_d16.5961
X-RAY DIFFRACTIONf_plane_restr0.0041
X-RAY DIFFRACTIONf_nbd_refined4.1281

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