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- PDB-3yas: HYDROXYNITRILE LYASE COMPLEXED WITH ACETONE -

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Basic information

Entry
Database: PDB / ID: 3yas
TitleHYDROXYNITRILE LYASE COMPLEXED WITH ACETONE
ComponentsPROTEIN (HYDROXYNITRILE LYASE)
KeywordsLYASE / OXYNITRILASE / CYANOGENESIS / CYANOHYDRIN FORMATION
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
ACETONE / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsZuegg, J. / Wagner, U.G. / Gugganig, M. / Kratky, C.
Citation
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.
#1: Journal: Proteins / Year: 1997
Title: Hydroxynitrile lyase from Hevea brasiliensis: molecular characterization and mechanism of enzyme catalysis.
Authors: Hasslacher, M. / Kratky, C. / Griengl, H. / Schwab, H. / Kohlwein, S.D.
#2: 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.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and preliminary X-ray diffraction studies of a hydroxynitrile lyase from Hevea brasiliensis.
Authors: Wagner, U.G. / Schall, M. / Hasslacher, M. / Hayn, M. / Griengl, H. / Schwab, H. / Kratky, C.
#4: Journal: J.Biol.Chem. / Year: 1996
Title: Molecular cloning of the full-length cDNA of (S)-hydroxynitrile lyase from Hevea brasiliensis. Functional expression in Escherichia coli and Saccharomyces cerevisiae and identification of an active site residue.
Authors: Hasslacher, M. / Schall, M. / Hayn, M. / Griengl, H. / Kohlwein, S.D. / Schwab, H.
History
DepositionMar 15, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Oct 13, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 13, 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 / 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 / _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: PROTEIN (HYDROXYNITRILE LYASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7056
Polymers29,2631
Non-polymers4425
Water6,053336
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (HYDROXYNITRILE LYASE)
hetero molecules

A: PROTEIN (HYDROXYNITRILE LYASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,41012
Polymers58,5252
Non-polymers88510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3470 Å2
ΔGint-86 kcal/mol
Surface area18900 Å2
MethodPISA, PQS
3
A: PROTEIN (HYDROXYNITRILE LYASE)
hetero molecules

A: PROTEIN (HYDROXYNITRILE LYASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,41012
Polymers58,5252
Non-polymers88510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2510 Å2
ΔGint-82 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.484, 106.708, 128.100
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-510-

HOH

21A-511-

HOH

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Components

#1: Protein PROTEIN (HYDROXYNITRILE LYASE) / OXYNITRILASE


Mass: 29262.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Gene: HNL / Organ: LEAF / Plasmid: BHIL-D2 / Gene (production host): HNL / 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: Chemical ChemComp-ACN / ACETONE


Mass: 58.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growpH: 7.5
Details: 0.1 M NATRIUM HEPES BUFFER PH=7.5 2 % PEG 400, 2.0 M AMMONIUM SULFATE, 20 DEGREES SOAKING CONDITIONS: 400 MM ACETONE SOLUTION.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 %PEG4001reservoir
22.0 Mammonium sulfate1reservoir
30.1 Msodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→16 Å / Num. obs: 27904 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 7 Å2 / Rsym value: 0.096 / Net I/σ(I): 7.3
Reflection
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.95 Å / % possible obs: 99 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YAS

1yas


Resolution: 1.85→16 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1372 4.9 %RANDOM
Rwork0.19 ---
obs-27904 98.8 %-
Displacement parametersBiso mean: 9.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.85→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 24 336 2417
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.9
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.263 115 4.2 %
Rwork0.249 2607 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19X.SOLTOPH19X.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 9.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.263 / % reflection Rfree: 4.2 % / Rfactor Rwork: 0.249

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