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- PDB-1sci: K236L mutant of hydroxynitrile lyase from Hevea brasiliensis -

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Basic information

Entry
Database: PDB / ID: 1sci
TitleK236L mutant of hydroxynitrile lyase from Hevea brasiliensis
Components(S)-acetone-cyanohydrin lyase
KeywordsLYASE / alpha-beta hydrolase fold / catalytic triad
Function / homology
Function and homology information


aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity / (S)-hydroxynitrile lyase / 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)-hydroxynitrile lyase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.18 Å
AuthorsGruber, K. / Gartler, G. / Krammer, B. / Schwab, H. / Kratky, C.
Citation
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.
#1: 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.
#2: 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.
#3: 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
DepositionFeb 12, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,6315
Polymers29,2471
Non-polymers3844
Water4,702261
1
A: (S)-acetone-cyanohydrin lyase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)59,26210
Polymers58,4932
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3000 Å2
ΔGint-100 kcal/mol
Surface area19340 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.741, 107.028, 128.683
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsdimer; the second part of the biological assembly is generated by the two fod axis: x, -y+1, -z.

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Components

#1: Protein (S)-acetone-cyanohydrin lyase / hydroxynitrile lyase


Mass: 29246.578 Da / Num. of mol.: 1 / Mutation: K236L
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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.47 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG 400, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 18, 2001
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→20 Å / Num. all: 17474 / Num. obs: 17474 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 13.3 Å2 / Rsym value: 0.033 / Net I/σ(I): 31.9
Reflection shellResolution: 2.18→2.26 Å / Mean I/σ(I) obs: 22.3 / Num. unique all: 1705 / Rsym value: 0.084 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2yas

2yas


Resolution: 2.18→19.91 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1875444.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: refinement against maximum likelihood target function
RfactorNum. reflection% reflectionSelection details
Rfree0.212 884 5.1 %RANDOM
Rwork0.171 ---
obs0.171 17447 99.5 %-
all-17447 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.6105 Å2 / ksol: 0.375276 e/Å3
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--1.66 Å20 Å2
3----1.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 2.18→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 20 261 2337
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.422
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 2.18→2.26 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.208 83 5.1 %
Rwork0.147 1540 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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