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- PDB-8jm3: Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A f... -

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Basic information

Entry
Database: PDB / ID: 8jm3
TitleEndo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A from Prunus communis complexed with 4H-benzo[d][1,3]dioxine-6-carbaldehyde
Components(R)-mandelonitrile lyase
KeywordsLYASE / Hydroxynitrile lyase / FAD / hydrocynanation
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION
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 from Prunus communis complexed with 4H-benzo[d][1,3]dioxine-6-carbaldehyde
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

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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)61,45011
Polymers58,9721
Non-polymers2,47810
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint15 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.648, 91.713, 129.724
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 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 α-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.: 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 , 5 types, 300 molecules

#3: Chemical ChemComp-FQ6 / 4H-1,3-benzodioxine-6-carbaldehyde / 4H-benzo[d][1,3]dioxine-6-carbaldehyde


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3 / 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
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: 0.97891 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 47153 / % possible obs: 99.9 % / Redundancy: 10.9 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.036 / Rrim(I) all: 0.12 / Χ2: 1.115 / Net I/σ(I): 5 / Num. measured all: 515252
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.9311.20.83923090.860.9620.2610.8790.488100
1.93-1.9711.20.71823190.90.9730.2240.7530.501100
1.97-2.0111.20.58623320.9270.9810.1830.6140.531100
2.01-2.0511.20.51323150.9340.9830.160.5370.566100
2.05-2.0911.10.44723190.9430.9850.140.4690.591100
2.09-2.1411.20.37423270.9610.990.1170.3930.663100
2.14-2.1911.10.34223260.9670.9920.1070.3580.725100
2.19-2.2510.90.29923430.9690.9920.0940.3130.74100
2.25-2.3210.60.25823100.9750.9940.0820.2710.84399.8
2.32-2.399.40.2323500.9790.9950.0780.2430.89199.9
2.39-2.4811.30.20823480.9840.9960.0640.2180.989100
2.48-2.5811.60.18423190.9860.9960.0560.1921.077100
2.58-2.711.40.16723810.9890.9970.0510.1751.192100
2.7-2.8411.30.14523270.990.9980.0450.1521.287100
2.84-3.0211.20.12823800.9920.9980.040.1351.482100
3.02-3.2510.70.11223680.9930.9980.0360.1181.78199.9
3.25-3.589.60.09723800.9950.9990.0320.1032.13799.8
3.58-4.0911.50.08724010.9960.9990.0270.0912.462100
4.09-5.16110.07224330.9970.9990.0230.0762.201100
5.16-50100.05225660.9970.9990.0170.0541.10899.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.46 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.803 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19474 2421 5.1 %RANDOM
Rwork0.15902 ---
obs0.16085 44669 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.149 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å2-0 Å2
2---0.95 Å20 Å2
3---1.13 Å2
Refinement stepCycle: 1 / Resolution: 1.9→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3948 0 161 296 4405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134222
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173818
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.6745779
X-RAY DIFFRACTIONr_angle_other_deg1.4221.5988810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5015513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70423.317202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44615613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0811518
X-RAY DIFFRACTIONr_chiral_restr0.0840.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024805
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02945
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_it2.5252.8652055
X-RAY DIFFRACTIONr_mcbond_other2.5212.8632054
X-RAY DIFFRACTIONr_mcangle_it3.2474.2812564
X-RAY DIFFRACTIONr_mcangle_other3.2464.2832565
X-RAY DIFFRACTIONr_scbond_it3.4843.2462167
X-RAY DIFFRACTIONr_scbond_other3.4793.242164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0474.7373209
X-RAY DIFFRACTIONr_long_range_B_refined6.1735.1014736
X-RAY DIFFRACTIONr_long_range_B_other6.17735.1084737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 173 -
Rwork0.206 3045 -
obs--94.23 %

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