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- PDB-1dwq: Crystal Structure of Hydroxynitrile Lyase from Manihot esculenta ... -

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Basic information

Entry
Database: PDB / ID: 1dwq
TitleCrystal Structure of Hydroxynitrile Lyase from Manihot esculenta in Complex with Substrates Acetone and Chloroacetone:Implications for the Mechanism of Cyanogenesis
ComponentsHYDROXYNITRILE LYASE
KeywordsHYDROXYNITRILE LYASE / CHLOROACETONE COMPLEX
Function / homology
Function and homology information


aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity / (S)-hydroxynitrile lyase
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
CHLOROACETONE / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesMANIHOT ESCULENTA (cassava)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLauble, H. / Forster, S. / Mielich, B. / Wajant, H. / Effenberger, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Hydroxynitrile Lyase from Manihot Esculenta in Complex with Substrates Acetone and Chloroacetone: Implications for the Mechanism of Cyanogenesis
Authors: Lauble, H. / Forster, S. / Miehlich, B. / Wajant, H. / Effenberger, F.
History
DepositionDec 10, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8753
Polymers59,7832
Non-polymers931
Water3,801211
1
A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE
hetero molecules

A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7506
Polymers119,5654
Non-polymers1852
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7640 Å2
ΔGint-35.9 kcal/mol
Surface area44170 Å2
MethodPQS
Unit cell
Length a, b, c (Å)104.500, 104.500, 189.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsBIOLOGICAL_UNIT: TETRAMER

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Components

#1: Protein HYDROXYNITRILE LYASE / (S)-ACETONE-CYANOHYDRIN LYASE / (S)-HYDROXYNITRILASE


Mass: 29891.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CHLOROACETONE COMPLEX / Source: (gene. exp.) MANIHOT ESCULENTA (cassava) / Description: RECOMBINANT PROTEIN / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52705, EC: 4.2.1.37
#2: Chemical ChemComp-ATO / CHLOROACETONE


Mass: 92.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5ClO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SWISSPROT ENTRY P52705 REPORTS THIS ENZYME TO BE EC 4.2.1.39, AND TO HAVE A HOMOTRIMERIC ...THE SWISSPROT ENTRY P52705 REPORTS THIS ENZYME TO BE EC 4.2.1.39, AND TO HAVE A HOMOTRIMERIC SUBUNIT STRUCTURE. THE CORRECT EC NUMBER IS 4.2.1.37 AND THE MOLECULE IS A TETRAMER.

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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: 4.3 Å3/Da / Density % sol: 71 %
Crystal growpH: 5.4 / Details: 0.1 M NACITRAT, PH 5.4, 6% PEG8000, 28% MPD
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Lauble, H., (1999) Acta Crystallogr., D55, 904.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
25 %PEG80001reservoir
316 %MPD1reservoir
4100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.905
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 54130 / % possible obs: 96.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.055 / Rsym value: 0.074 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.1 / % possible all: 98.2
Reflection
*PLUS
Num. measured all: 207542 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.159

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2 / Details: CHLOROACETONE COMPLEX
RfactorNum. reflection% reflection
Rfree0.244 5419 10 %
Rwork0.207 --
obs0.207 51519 97.4 %
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 5 211 4402
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
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
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6

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