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- PDB-8jm0: Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A f... -

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Basic information

Entry
Database: PDB / ID: 8jm0
TitleEndo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A from Prunus communis complexed with 2,2-dimethyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde from the cyanohydrin cleavage
Components(R)-mandelonitrile lyase
KeywordsLYASE / Hydroxynitrile lyase / FAD / hydrocynanation
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesPrunus dulcis (almond)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsZheng, Y.C. / Li, F.L. / Yu, H.L. / Xu, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A from Prunus communis complexed with 2,2-dimethyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde from the cyanohydrin cleavage
Authors: Zheng, Y.C. / Li, F.L. / Yu, H.L. / Xu, J.H.
History
DepositionJun 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Oct 8, 2025Group: Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / struct
Item: _audit_author.name / _citation.title ..._audit_author.name / _citation.title / _citation_author.name / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (R)-mandelonitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,34214
Polymers58,9721
Non-polymers3,37013
Water7,404411
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint21 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.491, 91.131, 130.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein (R)-mandelonitrile lyase


Mass: 58972.355 Da / Num. of mol.: 1 / Mutation: L331A
Source method: isolated from a genetically manipulated source
Details: Author stated the sequence reference is Genbank AAP84580.1, and the initial signal peptide (Met1 to Ser27) was exchanged into yeast alpha-factor subjected to cleavage during extracellular expression.
Source: (gene. exp.) Prunus dulcis (almond) / Gene: ALMOND_2B028509 / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: (R)-mandelonitrile lyase

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Sugars , 2 types, 8 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 416 molecules

#4: Chemical ChemComp-FQ3 / 2,2-dimethyl-4H-1,3-benzodioxine-6-carbaldehyde / 2,2-dimethyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde


Mass: 192.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: tris-bicine, 100 mM, pH 8.25; CaCl2, 60 mM; MgCl2, 60 mM; PEG 500MME, 24%, v/v; PEG 20000, 12%, w/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 56025 / % possible obs: 99.7 % / Redundancy: 12.1 % / CC1/2: 0.992 / CC star: 0.998 / Χ2: 0.938 / Net I/σ(I): 13.5
Reflection shellResolution: 1.79→1.83 Å / Redundancy: 11.6 % / Num. unique obs: 2744 / CC1/2: 0.727 / CC star: 0.918 / Χ2: 0.43 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→33.54 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.85 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1961 2773 5 %RANDOM
Rwork0.16373 ---
obs0.16536 53189 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.906 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å2-0 Å20 Å2
2---1.41 Å20 Å2
3---0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.79→33.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3981 0 221 411 4613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134310
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173885
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.6915898
X-RAY DIFFRACTIONr_angle_other_deg1.4261.6148975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7625515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10323.416202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1915614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7831517
X-RAY DIFFRACTIONr_chiral_restr0.0790.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024864
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02951
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8792.0662069
X-RAY DIFFRACTIONr_mcbond_other1.8772.0642068
X-RAY DIFFRACTIONr_mcangle_it2.7043.0832581
X-RAY DIFFRACTIONr_mcangle_other2.7033.0862582
X-RAY DIFFRACTIONr_scbond_it2.9062.5082241
X-RAY DIFFRACTIONr_scbond_other2.9052.5082242
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.383.6653318
X-RAY DIFFRACTIONr_long_range_B_refined5.59726.6524894
X-RAY DIFFRACTIONr_long_range_B_other5.46226.254803
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.794→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 185 -
Rwork0.251 3695 -
obs--94.43 %

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