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- PDB-2yas: HYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS COMPLEXED WITH RHODANIDE -

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Basic information

Entry
Database: PDB / ID: 2yas
TitleHYDROXYNITRILE LYASE FROM HEVEA BRASILIENSIS COMPLEXED WITH RHODANIDE
ComponentsPROTEIN (HYDROXYNITRILE LYASE)
KeywordsLYASE / OXYNITRILASE / CYANOGENESIS / CYANHYDRIN 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
THIOCYANATE ION / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.72 Å
AuthorsGruber, K. / 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: 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.
#2: 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.
#3: 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 11, 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_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 30, 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
Water6,017334
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 area3500 Å2
ΔGint-110 kcal/mol
Surface area19260 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 area2540 Å2
ΔGint-101 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.423, 106.771, 128.753
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-509-

HOH

21A-630-

HOH

31A-632-

HOH

41A-689-

HOH

51A-752-

HOH

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Components

#1: Protein PROTEIN (HYDROXYNITRILE LYASE) / OXYNITRILE LYASE


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-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 49 %
Crystal growpH: 7.5
Details: PH=7.5 2 % PEG 400, 2.0 M AMMONIUM SULFATE, 20 DEGREES.
Crystal
*PLUS
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: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9076
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9076 Å / Relative weight: 1
ReflectionResolution: 1.72→14 Å / Num. obs: 34663 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.066 / Net I/σ(I): 18.9
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 5.8 / Rsym value: 0.237 / % possible all: 99.6
Reflection
*PLUS
Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.237

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97model building
SHELXL-97refinement
SHELXL-97phasing
RefinementMethod to determine structure: OTHER
Starting model: 1YAS

1yas


Resolution: 1.72→14 Å / Num. parameters: 9757 / Num. restraintsaints: 8672 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 3465 11.1 %RANDOM
all0.1544 31167 --
obs0.1501 -97.7 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 2049 / Occupancy sum non hydrogen: 2411.5
Refinement stepCycle: LAST / Resolution: 1.72→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 23 334 2414
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.052
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.027
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.054
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 14 Å / σ(F): 0 / % reflection Rfree: 11.1 % / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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