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- PDB-8jm8: Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A f... -

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Basic information

Entry
Database: PDB / ID: 8jm8
TitleEndo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A from Prunus communis complexed with (R)-2-(2,2-dimethyl-4H-benzo[d][1,3]dioxin-6-yl)-2-hydroxyacetonitrile
Components(R)-mandelonitrile lyase
KeywordsLYASE / Hydroxynitrile lyase / FAD / hydrocynanation
Function / homology: / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesPrunus dulcis (almond)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 (R)-2-(2,2-dimethyl-4H-benzo[d][1,3]dioxin-6-yl)-2-hydroxyacetonitrile
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 5, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)61,76612
Polymers59,0001
Non-polymers2,76511
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint15 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.339, 90.442, 125.498
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: 59000.449 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, 6 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
#4: 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.: 5 / 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 , 5 types, 498 molecules

#3: Chemical ChemComp-E2Y / (R)-2-(2,2-dimethyl-4H-benzo[d][1,3]dioxin-6-yl)-2-hydroxyacetonitrile / (R)-alpha-Hydroxy-2,2-dimethyl-4H-1,3-benzodioxin-6-acetonitrile


Mass: 219.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13NO3 / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: tris-bicine, 100 mM, pH 8.5; CaCl2, 60 mM; MgCl2, 60 mM; PEG 500MME, 20%, v/v; PEG 20000, 10%, w/v
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 62650 / % possible obs: 99.8 % / Redundancy: 6.1 % / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Χ2: 1.038 / Net I/σ(I): 6.3 / Num. measured all: 382037
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.736.10.20530590.9590.990.090.2240.45799.9
1.73-1.7660.10831000.9880.9970.0480.1180.19499.8
1.76-1.7960.09830540.990.9970.0440.1080.20899.9
1.79-1.835.70.09231120.990.9970.0420.1010.23399.5
1.83-1.875.50.08430820.9910.9980.0390.0930.24999.9
1.87-1.915.70.21431080.7740.9340.10.2371.08599.6
1.91-1.966.20.29430990.8820.9680.1260.3211.64899.8
1.96-2.026.20.06731010.9930.9980.030.0740.31399.9
2.02-2.0760.2430820.890.970.1050.2621.63599.6
2.07-2.146.10.0731400.9890.9970.0310.0770.44399.8
2.14-2.226.20.05830820.9950.9990.0250.0630.39699.7
2.22-2.315.80.231070.7340.920.0920.2211.66999.7
2.31-2.415.80.05731300.9940.9980.0260.0630.56699.6
2.41-2.546.30.09531280.9930.9980.0390.1030.69299.9
2.54-2.76.60.08231330.9890.9970.0350.091.199.9
2.7-2.916.60.05531790.9940.9980.0230.060.77100
2.91-3.26.50.05231500.9930.9980.0220.0570.917100
3.2-3.665.90.06831830.990.9970.030.0741.40999.8
3.66-4.616.60.05532130.9940.9990.0230.061.4999.2
4.61-506.10.06734080.9620.990.0290.0734.776100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→45.96 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 1.725 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21375 3239 5.2 %RANDOM
Rwork0.17729 59295 --
all0.179 ---
obs0.17917 59295 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.7→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 182 493 4621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134230
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173835
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.6815788
X-RAY DIFFRACTIONr_angle_other_deg1.5051.6028847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.515511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05223.467199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54815612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7011517
X-RAY DIFFRACTIONr_chiral_restr0.0960.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02941
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_it1.1411.1482053
X-RAY DIFFRACTIONr_mcbond_other1.141.1462052
X-RAY DIFFRACTIONr_mcangle_it1.6781.7172561
X-RAY DIFFRACTIONr_mcangle_other1.6781.7182562
X-RAY DIFFRACTIONr_scbond_it2.051.4072177
X-RAY DIFFRACTIONr_scbond_other2.0491.4082178
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0752.0363228
X-RAY DIFFRACTIONr_long_range_B_refined5.62315.8984928
X-RAY DIFFRACTIONr_long_range_B_other5.62215.9054929
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.741 Å
RfactorNum. reflection% reflection
Rfree0.181 217 -
Rwork0.155 4090 -
obs--94 %

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