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

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Basic information

Entry
Database: PDB / ID: 1dwo
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 / ACETONE 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
ACETONE / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesMANIHOT ESCULENTA (cassava)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLauble, H. / Forster, S. / Miehlich, 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 / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)59,7283
Polymers59,6702
Non-polymers581
Water4,882271
1
A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE
hetero molecules

A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4576
Polymers119,3414
Non-polymers1162
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6710 Å2
ΔGint-46.4 kcal/mol
Surface area44170 Å2
MethodPQS
Unit cell
Length a, b, c (Å)105.500, 105.500, 188.500
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: 29835.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ACETONE 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-ACN / ACETONE


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


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
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: 52853 / % possible obs: 97.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.054 / Rsym value: 0.068 / Net I/σ(I): 8.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.2 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 215742 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.141

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
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
RfactorNum. reflection% reflection
Rfree0.252 5303 10 %
Rwork0.192 --
obs0.192 52853 97 %
Displacement parametersBiso mean: 26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.25 Å
Luzzati d res low-8 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4178 0 4 271 4453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.2
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

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