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- PDB-1sc9: Hydroxynitrile Lyase from Hevea brasiliensis in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 1sc9
TitleHydroxynitrile Lyase from Hevea brasiliensis in complex with the natural substrate acetone cyanohydrin
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
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
2-HYDROXY-2-METHYLPROPANENITRILE / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 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 1.4Oct 25, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,5404
Polymers29,2631
Non-polymers2773
Water5,585310
1
A: (S)-acetone-cyanohydrin lyase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)59,0808
Polymers58,5252
Non-polymers5546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area2970 Å2
ΔGint-52 kcal/mol
Surface area18890 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)47.393, 106.455, 127.988
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-808-

HOH

21A-809-

HOH

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: 29262.598 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CNH / 2-HYDROXY-2-METHYLPROPANENITRILE / ACETONE CYANOHYDRIN / Acetone cyanohydrin


Mass: 85.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.37 Å3/Da / Density % sol: 47.79 %
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 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: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 30106 / Num. obs: 30106 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.069 / Net I/σ(I): 19.4
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 6.1 / Num. unique all: 1931 / Rsym value: 0.252 / % possible all: 96.9

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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: 1.8→28.41 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1958997.55 / 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
Rfree0.189 1523 5.1 %RANDOM
Rwork0.167 ---
obs0.167 30083 98.9 %-
all-30106 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.7011 Å2 / ksol: 0.386387 e/Å3
Displacement parametersBiso mean: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å20 Å2
2--2.19 Å20 Å2
3----4.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 16 310 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it0.911.5
X-RAY DIFFRACTIONc_mcangle_it1.212
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.552.5
LS refinement shellResolution: 1.8→1.84 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.214 91 5 %
Rwork0.191 1724 -
obs-1931 89.8 %
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 DIFFRACTION4ACN.PARAMACN.TOP

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