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- PDB-1e8d: MECHANISTIC ASPECTS OF CYANOGENESIS FROM ACTIVE SITE MUTANT SER80... -

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Basic information

Entry
Database: PDB / ID: 1e8d
TitleMECHANISTIC ASPECTS OF CYANOGENESIS FROM ACTIVE SITE MUTANT SER80ALA OF HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA IN COMPLEX WITH ACETONE CYANOHYDRIN
ComponentsHYDROXYNITRILE LYASE
KeywordsLYASE / HYDROXYNITRILE LYASE / ACTIVE SITE MUTANT / ACETONE CYANOHYDRIN 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
2-HYDROXY-2-METHYLPROPANENITRILE / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesMANIHOT ESCULENTA (cassava)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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. / Forster, 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 19, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2001Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9796
Polymers59,6382
Non-polymers3404
Water4,918273
1
A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE
hetero molecules

A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,95812
Polymers119,2774
Non-polymers6818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8150 Å2
ΔGint-53 kcal/mol
Surface area44330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.900, 105.900, 187.800
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
Details: ACETONE CYANOHYDRIN COMPLEX / Source: (gene. exp.) MANIHOT ESCULENTA (cassava) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52705, EC: 4.2.1.37
#2: Chemical
ChemComp-CNH / 2-HYDROXY-2-METHYLPROPANENITRILE / ACETONE CYANOHYDRIN


Mass: 85.104 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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 NA CITRATE, 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: 2.2→15 Å / Num. obs: 52736 / % possible obs: 97.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.068 / Net I/σ(I): 8.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.135 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 211247 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.135

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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 1E89

1e89


Resolution: 2.2→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
Rfree0.238 5079 10.1 %RANDOM
Rwork0.186 ---
obs0.186 50187 93.6 %-
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-8 Å
Luzzati sigma a0.16 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 24 273 4473
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.951.5
X-RAY DIFFRACTIONx_mcangle_it2.842
X-RAY DIFFRACTIONx_scbond_it4.112
X-RAY DIFFRACTIONx_scangle_it6.162.5
LS refinement shellResolution: 2.2→2.33 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 799 9.8 %
Rwork0.231 7375 -
obs--93.1 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18

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