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- PDB-1eb9: Structure Determinants of Substrate Specificity of Hydroxynitrile... -

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Basic information

Entry
Database: PDB / ID: 1eb9
TitleStructure Determinants of Substrate Specificity of Hydroxynitrile Lyase from Manihot esculenta
ComponentsHYDROXYNITRILE LYASE
KeywordsLYASE / HYDROXYNITRILE LYASE / SUBSTRATE SPECIFICITY / ACTIVE-SITE TUNNEL MUTANT
Function / homology
Function and homology information


(S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity / jasmonic acid metabolic process / methyl salicylate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process / methyl indole-3-acetate esterase 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
P-HYDROXYBENZALDEHYDE / (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. / Kobler, C. / Wajant, H. / Effenberger, F.
Citation
Journal: Protein Sci. / Year: 2002
Title: Structure Determinants of Substrate Specificity of Hydroxynitrile Lyase from Manihot Esculenta.
Authors: Lauble, H. / Miehlich, B. / Foerster, S. / Kobler, C. / 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
DepositionJul 24, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2002Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9296
Polymers59,4402
Non-polymers4884
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)119,85712
Polymers118,8804
Non-polymers9778
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)106.340, 106.340, 188.840
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)-HYDROXYNITRILE LYASE / (S)-HYDROXYNITRILASE / OXYNITRILASE / HYDROXYNITRILE LYASE


Mass: 29720.080 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: Chemical
ChemComp-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B ENGINEERED MUTATION TRP127ALA CHAIN A, B RESIDUES -4 TO 1 ARE CLONING ARTEFACTS KNOWN TO ...CHAIN A, B ENGINEERED MUTATION TRP127ALA CHAIN A, B RESIDUES -4 TO 1 ARE CLONING ARTEFACTS KNOWN TO BE INVOLVED IN THE RELEASE OF HCN FROM INJURED TISSUES (CYANOGENESIS)

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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, 5% PEG8000, 28% MPD
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: Lauble, H., (1999) Acta Crystallogr.,Sect.D, 55, 904.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 %PEG80001reservoir
216 %MPD1reservoir
3100 mMsodium citrate1reservoirpH5.4
432 mg/mlprotein1drop
510 mMsodium citrate1droppH5.4

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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: 63477 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 19.2
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 5.1 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. measured all: 415040
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 99.9 %

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Processing

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

1dwp


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
Rfree0.244 6079 10 %RANDOM
Rwork0.197 ---
obs0.197 60760 97.1 %-
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-8 Å
Luzzati sigma a0.16 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4160 0 36 271 4467
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_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.12
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.831.5
X-RAY DIFFRACTIONx_mcangle_it2.772
X-RAY DIFFRACTIONx_scbond_it3.922
X-RAY DIFFRACTIONx_scangle_it6.042.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 976 10.1 %
Rwork0.252 8705 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHBA.PROTOPHBA.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.12
LS refinement shell
*PLUS
Rfactor obs: 0.252

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