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- PDB-8jm5: Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A/S... -

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Basic information

Entry
Database: PDB / ID: 8jm5
TitleEndo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A/S333V/P340L from Prunus communis
Components(R)-mandelonitrile lyase
KeywordsLYASE / Hydroxynitrile lyase / FAD / hydrocynanation
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesPrunus dulcis (almond)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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/S333V/P340L from Prunus communis
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 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,28110
Polymers59,0001
Non-polymers2,2819
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint12 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.492, 90.950, 130.435
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 / Sugars , 2 types, 7 molecules B

#1: Protein (R)-mandelonitrile lyase


Mass: 59000.449 Da / Num. of mol.: 1 / Mutation: L331A,S333V,P340L
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): X / References: (R)-mandelonitrile lyase
#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.: 6 / 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 , 4 types, 566 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.49 Å3/Da / Density % sol: 50.56 %
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: 0.97854 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 47405 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.037 / Rrim(I) all: 0.134 / Χ2: 0.894 / Net I/σ(I): 5 / Num. measured all: 616877
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.9313.10.83423150.9030.9740.2380.8681.255100
1.93-1.9713.10.58723400.9490.9870.1670.6110.68100
1.97-2.0112.90.45723400.9690.9920.1330.4760.517100
2.01-2.0512.20.41223290.9640.9910.1220.4310.567100
2.05-2.0912.50.61323290.9190.9790.1810.641.539100
2.09-2.1413.60.33623420.9740.9930.0940.350.665100
2.14-2.1913.60.29423460.9830.9960.0830.3050.61100
2.19-2.2513.50.43423720.9790.9950.1230.4511.248100
2.25-2.3213.30.27323110.9830.9960.0770.2840.78100
2.32-2.39130.21423560.9860.9960.0620.2230.668100
2.39-2.4812.20.18923620.9890.9970.0560.1970.682100
2.48-2.5812.90.20523360.9910.9980.0580.2130.786100
2.58-2.713.60.19223650.990.9980.0540.20.96100
2.7-2.8413.40.15823570.9940.9980.0440.1640.753100
2.84-3.0213.40.12423740.9930.9980.0350.1290.803100
3.02-3.2512.20.1123990.9940.9980.0330.1150.82199.9
3.25-3.5813.60.10723860.9940.9980.030.1121.011100
3.58-4.0913.40.10624250.9950.9990.030.111.158100
4.09-5.1612.40.07724250.9950.9990.0230.080.80799.8
5.16-5012.50.08825960.9910.9980.0260.0921.51399.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.32 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.776 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19031 2359 5.1 %RANDOM
Rwork0.15189 44000 --
all0.154 ---
obs0.15387 44000 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.022 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-0 Å2
2---0.17 Å20 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3984 0 148 563 4695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134236
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173849
X-RAY DIFFRACTIONr_angle_refined_deg1.7781.6695795
X-RAY DIFFRACTIONr_angle_other_deg1.4241.5988876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5785515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74123.416202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87815617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8061517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024823
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02950
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_it1.7511.8532069
X-RAY DIFFRACTIONr_mcbond_other1.7491.8512068
X-RAY DIFFRACTIONr_mcangle_it2.5682.7632581
X-RAY DIFFRACTIONr_mcangle_other2.5672.7652582
X-RAY DIFFRACTIONr_scbond_it2.7692.2172167
X-RAY DIFFRACTIONr_scbond_other2.7692.2172168
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2033.2273215
X-RAY DIFFRACTIONr_long_range_B_refined6.24124.7324996
X-RAY DIFFRACTIONr_long_range_B_other6.24124.7374997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.948 Å
RfactorNum. reflection% reflection
Rfree0.234 133 -
Rwork0.216 2747 -
obs--83.58 %

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