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- PDB-6lr8: Mutant L331A of deglycosylated hydroxynitrile lyase isozyme 5 fro... -

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Basic information

Entry
Database: PDB / ID: 6lr8
TitleMutant L331A of deglycosylated hydroxynitrile lyase isozyme 5 from Prunus communis
ComponentsPREDICTED: (R)-mandelonitrile lyase
KeywordsLYASE / FAD-dependent hydroxynitrile lyase
Function / homology
Function and homology information


mandelonitrile lyase activity / (R)-mandelonitrile lyase / oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Cholesterol Oxidase; domain 2 - #40 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Flavin amine oxidase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase ...Cholesterol Oxidase; domain 2 - #40 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 1. / GMC oxidoreductases signature 2. / Glucose-methanol-choline oxidoreductase / Flavin amine oxidase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / (R)-mandelonitrile lyase / (R)-mandelonitrile lyase 1
Similarity search - Component
Biological speciesPrunus dulcis (almond)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.595 Å
AuthorsZheng, Y.-C. / Xu, J.-H.
CitationJournal: Acs Catalysis / Year: 2020
Title: Structure-Guided Tuning of a Hydroxynitrile Lyase to Accept Rigid Pharmaco Aldehydes.
Authors: Zheng, Y.C. / Li, F.L. / Lin, Z.M. / Lin, G.Q. / Hong, R. / Yu, H.L. / Xu, J.H.
History
DepositionJan 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,2819
Polymers58,7441
Non-polymers2,5378
Water13,691760
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint22 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.553, 91.162, 130.924
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PREDICTED: (R)-mandelonitrile lyase


Mass: 58744.102 Da / Num. of mol.: 1 / Mutation: L331A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prunus dulcis (almond) / Gene: ALMOND_2B028509 / Plasmid: pPICZ / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: A0A5E4GBK6, UniProt: O24243*PLUS
#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-Glycam 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
[]{[(4+1)][b-D-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.: 6
Source method: isolated from a genetically manipulated source
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
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsM532 is maybe a natural mutagenesis of the AOA5E4GBK6 since authors have confirmed that the initial ...M532 is maybe a natural mutagenesis of the AOA5E4GBK6 since authors have confirmed that the initial sequence which was amplified by PCR reaction from the cDNA library of the Prunus communis.

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 289 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: 8.25-8.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.595→50 Å / Num. obs: 78549 / % possible obs: 98.8 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.025 / Rrim(I) all: 0.089 / Χ2: 0.965 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6312.40.39338110.950.1150.410.81298.2
1.63-1.6612.40.36837990.960.1080.3840.82396.7
1.66-1.6912.20.3238210.9630.0950.3350.83698.3
1.69-1.7212.20.28938440.9710.0850.3020.86797.3
1.72-1.7611.90.25738520.9740.0770.2690.90597.9
1.76-1.811.70.22938430.9760.0690.2390.97298.4
1.8-1.8511.40.20838880.9790.0630.2171.03498.4
1.85-1.910.50.1938770.9810.0590.1991.16398.4
1.9-1.9512.20.17838940.9850.0530.1861.16399.4
1.95-2.0212.20.15839100.9850.0470.1651.16199.3
2.02-2.0912.10.14639290.9880.0430.1531.20799.4
2.09-2.1712.10.13339470.990.0390.1391.22299.4
2.17-2.27120.12339330.9920.0360.1281.18799.6
2.27-2.3911.10.11239260.9910.0340.1181.16698.8
2.39-2.5412.20.10339750.9930.030.1071.06699.6
2.54-2.7412.80.09239750.9950.0270.0960.94999.7
2.74-3.0112.70.08139880.9950.0230.0850.86699.8
3.01-3.45120.07140060.9970.0210.0740.87199.1
3.45-4.3413.30.05640880.9980.0160.0580.6799.8
4.34-5012.50.04742430.9970.0140.0490.51199.1

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JBY

6jby


Resolution: 1.595→41.313 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.04
RfactorNum. reflection% reflection
Rfree0.1735 4002 5.1 %
Rwork0.1526 --
obs0.1536 78405 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.77 Å2 / Biso mean: 16.6967 Å2 / Biso min: 5.88 Å2
Refinement stepCycle: final / Resolution: 1.595→41.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3989 0 165 760 4914
Biso mean--23.43 28.69 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064266
X-RAY DIFFRACTIONf_angle_d0.925845
X-RAY DIFFRACTIONf_chiral_restr0.055674
X-RAY DIFFRACTIONf_plane_restr0.006749
X-RAY DIFFRACTIONf_dihedral_angle_d7.8792444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.595-1.61380.16361110.1549213284
1.6138-1.63350.1881500.1525247197
1.6335-1.65410.19891420.1571253296
1.6541-1.67590.18511380.1559249099
1.6759-1.69890.17991490.1579249197
1.6989-1.72310.18041210.1567254497
1.7231-1.74890.18441130.1544254498
1.7489-1.77620.17261390.1515252297
1.7762-1.80530.19071220.1532253699
1.8053-1.83640.20411380.1581256498
1.8364-1.8698132253899
1.8698-1.90580.16281290.1565256198
1.9058-1.94470.19611320.1563258199
1.9447-1.9870.17121420.154257999
1.987-2.03320.17331500.15262555100
2.0332-2.08410.18351460.15256899
2.0841-2.14040.19271230.1461260699
2.1404-2.20340.15921390.14672575100
2.2034-2.27450.16731320.1505259899
2.2745-2.35580.20471330.1502261099
2.3558-2.45010.16711360.1523257699
2.4501-2.56160.18471370.1542608100
2.5616-2.69661552609100
2.6966-2.86550.17091150.16272653100
2.8655-3.08670.16391440.1612619100
3.0867-3.39720.16271470.15532629100
3.3972-3.88850.16131490.1403265799
3.8885-4.89780.14521700.12622672100
4.8978-41.3130.22921680.1772278399

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