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- PDB-1yb6: Hydroxynitrile lyase from hevea brasiliensis in complex with mand... -

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Basic information

Entry
Database: PDB / ID: 1yb6
TitleHydroxynitrile lyase from hevea brasiliensis in complex with mandelonitrile
Components(S)-acetone-cyanohydrin lyase
KeywordsLYASE / ALPHA-BETA HYDROLASE FOLD / SUBSTRATE COMPLEX / CATALYTIC TRIAD
Function / homology
Function and homology information


(S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity / jasmonic acid metabolic process / methyl salicylate esterase activity / methyl indole-3-acetate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / 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
(S)-MANDELIC ACID NITRILE / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.54 Å
AuthorsGruber, K. / Gartler, G. / Kratky, C.
Citation
Journal: J.Biotechnol. / Year: 2007
Title: Structural determinants of the enantioselectivity of the hydroxynitrile lyase from Hevea brasiliensis
Authors: Gartler, G. / Kratky, C. / Gruber, K.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Reaction Mechanism of Hydroxynitrile Lyases of the Alpha/Beta-Hydrolase Superfamily: The Three-Dimensional Structure of the Transient Enzyme-Substrate Complex Certifies the Crucial Role of Lys236
Authors: Gruber, K. / Gartler, G. / Krammer, B. / Schwab, H. / Kratky, C.
#2: Journal: Biol.Chem. / Year: 1999
Title: Atomic Resolution Crystal Structure of Hydroxynitrile Lyase from Hevea Brasiliensis
Authors: Gruber, K. / Gugganig, M. / Wagner, U.G. / Kratky, C.
#3: Journal: Protein Sci. / Year: 1999
Title: Three-Dimensional Structures of Enzyme-Substrate Complexes of the Hydroxynitrile Lyase from Hevea Brasiliensis
Authors: Zuegg, J. / Gruber, K. / Gugganig, M. / Wagner, U.G. / Kratky, C.
#4: Journal: Structure / Year: 1996
Title: Mechanism of Cyanogenesis: The Crystal Structure of Hydroxynitrile Lyase from Hevea Brasiliensis
Authors: Wagner, U.G. / Hasslacher, M. / Griengl, H. / Schwab, H. / Kratky, C.
History
DepositionDec 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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: (S)-acetone-cyanohydrin lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4574
Polymers29,1311
Non-polymers3253
Water5,152286
1
A: (S)-acetone-cyanohydrin lyase
hetero molecules

A: (S)-acetone-cyanohydrin lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9138
Polymers58,2632
Non-polymers6516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3130 Å2
ΔGint-48 kcal/mol
Surface area18960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)47.362, 106.553, 128.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

21A-769-

HOH

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Components

#1: Protein (S)-acetone-cyanohydrin lyase / E.C.4.1.2.39 / (S)-hydroxynitrile lyase / (S)-hydroxynitrilase / Oxynitrilase


Mass: 29131.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Tissue: LEAF / Gene: HNL / Plasmid: BHIL-D2 / Production host: Pichia pastoris (fungus) / References: UniProt: P52704, EC: 4.1.2.39
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MNN / (S)-MANDELIC ACID NITRILE / (S)-HYDROXY(PHENYL)ACETONITRILE


Mass: 133.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: AMMONIUM SULFATE, PEG 400, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8426 / Wavelength: 0.8426 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 8, 2001
RadiationMonochromator: UNKNOWN / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8426 Å / Relative weight: 1
ReflectionResolution: 1.54→23.68 Å / Num. all: 46599 / Num. obs: 46599 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.023 / Net I/σ(I): 28.1
Reflection shellResolution: 1.54→1.58 Å / Mean I/σ(I) obs: 7.6 / Rsym value: 0.098 / % possible all: 96

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2YAS

2yas


Resolution: 1.54→23.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1782074.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2365 5.1 %RANDOM
Rwork0.167 ---
all0.167 46514 --
obs0.167 46514 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.7808 Å2 / ksol: 0.378627 e/Å3
Displacement parametersBiso mean: 14.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2--0.53 Å20 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.15 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 1.54→23.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 20 286 2363
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.831.5
X-RAY DIFFRACTIONc_mcangle_it1.212
X-RAY DIFFRACTIONc_scbond_it1.712
X-RAY DIFFRACTIONc_scangle_it2.472.5
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.188 151 4.8 %
Rwork0.171 3015 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4MN.PARMN.TOP

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