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- PDB-1e89: ON THE MECHANISM OF CYANOGENESIS CATALYZED BY HYDROXYNITRILE LYAS... -

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Basic information

Entry
Database: PDB / ID: 1.0E+89
TitleON THE MECHANISM OF CYANOGENESIS CATALYZED BY HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA. CRYSTAL STRUCTURE OF ACTIVE SITE MUTANT SER80ALA IN COMPLEX WITH ACETONE CYANOHYDRIN
ComponentsHYDROXYNITRILE LYASE
KeywordsLYASE / HYDROXYNITRILE LYASE / ACTIVE SITE MUTANT / ACETONE CYANOHYDRIN COMPLEX
Function / homology
Function and homology information


(S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity
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 speciesMANIHOT ESCULENTA (cassava)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLauble, H. / Miehlich, B. / Foerster, S. / Wajant, H. / Effenberger, F.
Citation
Journal: Protein Sci. / Year: 2001
Title: Mechanistic Aspects of Cyanogenesis from Active-Site Mutant Ser80Ala of Hydroxynitrile Lyase from Manihot Esculenta in Complex with Acetone Cyanohydrin
Authors: Lauble, H. / Miehlich, B. / Foerster, S. / Wajant, H. / Effenberger, F.
#1: Journal: 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. / Foerster, S. / Miehlich, B. / Wajant, H. / Effenberger, F.
History
DepositionSep 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE


Theoretical massNumber of molelcules
Total (without water)59,6382
Polymers59,6382
Non-polymers00
Water7,674426
1
A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE

A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE


Theoretical massNumber of molelcules
Total (without water)119,2774
Polymers119,2774
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)106.180, 106.180, 188.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 29819.209 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MANIHOT ESCULENTA (cassava) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52705, EC: 4.2.1.37
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B: CONTAINS ENGINEERED MUTATION S80A. RESIDUES -4 TO 1 ARE CLONING ARTEFACTS

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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: 4.5 Å3/Da / Density % sol: 71 %
Crystal growpH: 4.8 / Details: 0.1 M NACITRAT, PH 4.8, 6% PEG8000, 28% MPD
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Lauble, H., (1999) Acta Crystallogr.,Sect.D, 55, 904.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 %PEG80001reservoir
216 %MPD1reservoir
3100 mMsodium citrate1reservoir
430 mg/mlprotein1drop

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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: 2.1→20 Å / Num. obs: 63336 / % possible obs: 96.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.065 / Net I/σ(I): 8.8
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.141 / % possible all: 98.4
Reflection
*PLUS
Num. measured all: 265511 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.141

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DWO

1dwo


Resolution: 2.1→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.219 6024 10 %RANDOM
Rwork0.18 ---
obs0.18 60467 97.3 %-
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-8 Å
Luzzati sigma a0.15 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 0 426 4602
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.8
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_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.581.5
X-RAY DIFFRACTIONx_mcangle_it2.332
X-RAY DIFFRACTIONx_scbond_it3.532
X-RAY DIFFRACTIONx_scangle_it5.422.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 951 9.8 %
Rwork0.229 8746 -
obs--94.9 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13

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