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- PDB-7yas: HYDROXYNITRILE LYASE, LOW TEMPERATURE NATIVE STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 7yas
TitleHYDROXYNITRILE LYASE, LOW TEMPERATURE NATIVE STRUCTURE
ComponentsPROTEIN (HYDROXYNITRILE LYASE)
KeywordsLYASE / OXYNITRILASE / CYANOGENESIS / CYANHYDRIN FORMATION / COMPLEX (LYASE-PEPTIDE)
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 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
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Sep 20, 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)29,8816
Polymers29,2631
Non-polymers6195
Water5,441302
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)59,76212
Polymers58,5252
Non-polymers1,23710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3200 Å2
ΔGint-77 kcal/mol
Surface area19760 Å2
MethodPISA, PQS
3
A: PROTEIN (HYDROXYNITRILE LYASE)
hetero molecules

A: PROTEIN (HYDROXYNITRILE LYASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,76212
Polymers58,5252
Non-polymers1,23710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2360 Å2
ΔGint-65 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.529, 106.434, 128.381
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-490-

HOH

21A-491-

HOH

31A-492-

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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 7.5
Details: 0.1 M NATRIUM HEPES BUFFER PH=7.5 2 % PEG 400, 2.0 M AMMONIUM SULFATE, 20 DEGREES.
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: ELETTRA / Beamline: 5.2R / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.75→28 Å / Num. obs: 30389 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.037 / Net I/σ(I): 16
Reflection
*PLUS
Rmerge(I) obs: 0.037
Reflection shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.81 Å / % possible obs: 97.8 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 6.6

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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: 1.75→28 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE-R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1506 5 %RANDOM
Rwork0.191 ---
obs-30389 91.6 %-
Displacement parametersBiso mean: 11.2 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 36 302 2395
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_deg2.08
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 1.75→1.83 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.232 186 4.9 %
Rwork0.233 3804 -
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
Lowest resolution: 28 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
LS refinement shell
*PLUS
Rfactor Rfree: 0.232 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.233

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