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- PDB-8jm1: Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A f... -

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Basic information

Entry
Database: PDB / ID: 8jm1
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 / FAD / hydrocyanation / isozyme / complex
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / : / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesPrunus dulcis (almond)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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.
History
DepositionJun 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,11315
Polymers58,9721
Non-polymers3,14114
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint19 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.711, 91.485, 131.370
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, 9 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
#2: 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.: 8 / 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, 200 molecules

#3: 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
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


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


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.25
Details: tris-bicine, 100 mM, pH 8.25; CaCl2, 60 mM; MgCl2, 60 mM; PEG 500MME, 24%, v/v; PEG 20000, 12%, w/v
PH range: 8.25-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 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: 2.3→50 Å / Num. obs: 25370 / % possible obs: 93.3 % / Redundancy: 4 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.024 / Rpim(I) all: 0.013 / Rrim(I) all: 0.028 / Χ2: 0.852 / Net I/σ(I): 30.6 / Num. measured all: 101970
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.343.70.03112690.9970.9990.0180.0360.71195.7
2.34-2.383.70.03112780.9970.9990.0180.0360.71195.8
2.38-2.433.60.02912340.9970.9990.0170.0340.70293.4
2.43-2.483.70.02911410.9980.9990.0170.0340.74283.2
2.48-2.533.90.02811250.9980.9990.0160.0320.73184.6
2.53-2.594.10.02712800.99810.0150.0310.70696.4
2.59-2.663.90.0312470.9970.9990.0180.0350.92294.5
2.66-2.7340.03313160.9960.9990.0190.0381.18397.3
2.73-2.814.30.02513050.99810.0130.0280.72197.8
2.81-2.94.30.02413240.99910.0130.0270.69898.4
2.9-34.30.02312900.99910.0120.0260.74396.7
3-3.124.30.02213250.99910.0120.0250.75497.2
3.12-3.264.30.02313280.99910.0120.0260.80597.3
3.26-3.444.10.02512880.9980.9990.0140.0291.03296.3
3.44-3.654.10.02413200.99810.0130.0271.04697.2
3.65-3.9340.02513020.99810.0140.0291.2795.5
3.93-4.3340.02213060.99810.0120.0250.95493.8
4.33-4.9540.02210850.9980.9990.0120.0260.9577.6
4.95-6.244.30.02213750.99910.0120.0250.82798.1
6.24-503.80.02312320.99810.0130.0270.79481.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→30.91 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.197 1249 4.93 %
Rwork0.1633 --
obs0.1649 25349 93.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→30.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 205 194 4345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084246
X-RAY DIFFRACTIONf_angle_d0.965795
X-RAY DIFFRACTIONf_dihedral_angle_d12.176630
X-RAY DIFFRACTIONf_chiral_restr0.084670
X-RAY DIFFRACTIONf_plane_restr0.007735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.40.2551480.17782602X-RAY DIFFRACTION93
2.4-2.510.20381350.17872465X-RAY DIFFRACTION87
2.51-2.640.23331280.17242629X-RAY DIFFRACTION93
2.64-2.80.21751350.18242760X-RAY DIFFRACTION97
2.8-3.020.24521420.18212775X-RAY DIFFRACTION98
3.02-3.320.19181370.17682811X-RAY DIFFRACTION97
3.32-3.80.20391280.15662798X-RAY DIFFRACTION97
3.8-4.790.16041430.13412562X-RAY DIFFRACTION89
4.79-100.17811530.16162698X-RAY DIFFRACTION89

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