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- PDB-6jby: Crystal structure of endo-deglycosylated hydroxynitrile lyase iso... -

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Basic information

Entry
Database: PDB / ID: 6jby
TitleCrystal structure of endo-deglycosylated hydroxynitrile lyase isozyme 5 of Prunus communis
ComponentsHnl isoenzyme 5
KeywordsLYASE / Endo-deglycosylated / GMC oxidoreductases N and C superfamily / Flavoprotein / Complex
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 ...: / 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 1
Similarity search - Component
Biological speciesPrunus dulcis (almond)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZheng, Y.C. / Li, F.L. / Yu, H.L. / 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 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 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
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.3Mar 5, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hnl isoenzyme 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5038
Polymers59,1871
Non-polymers2,3167
Water12,088671
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint16 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.525, 91.307, 132.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hnl isoenzyme 5


Mass: 59186.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prunus dulcis (almond) / Gene: hnl5 / Production host: Komagataella pastoris (fungus) / References: UniProt: O24243*PLUS, (R)-mandelonitrile lyase
#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.: 5
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: isolated from a genetically manipulated source
Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris-bicine, calcium chloride, magnesium chloride, PEG 550MME, PEG 20000
PH range: 8.3-8.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 79762 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.031 / Rrim(I) all: 0.114 / Rsym value: 0.109 / Χ2: 0.993 / Net I/σ(I): 20.74
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 8.86 / Num. unique obs: 3877 / CC1/2: 0.973 / Rpim(I) all: 0.087 / Rrim(I) all: 0.321 / Rsym value: 0.309 / Χ2: 0.933 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12-2829-000)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EB4

5eb4


Resolution: 1.6→46.37 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.43
RfactorNum. reflection% reflection
Rfree0.1828 4040 5.07 %
Rwork0.158 --
obs0.1593 79649 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 53 671 4828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064265
X-RAY DIFFRACTIONf_angle_d0.9085846
X-RAY DIFFRACTIONf_dihedral_angle_d7.2622455
X-RAY DIFFRACTIONf_chiral_restr0.057675
X-RAY DIFFRACTIONf_plane_restr0.006752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6002-1.6190.2111400.1632460X-RAY DIFFRACTION97
1.619-1.63870.19181300.16372591X-RAY DIFFRACTION100
1.6387-1.65950.20381370.16612591X-RAY DIFFRACTION100
1.6595-1.68130.2331280.16062572X-RAY DIFFRACTION100
1.6813-1.70430.1871260.15812605X-RAY DIFFRACTION100
1.7043-1.72870.20161440.15882564X-RAY DIFFRACTION100
1.7287-1.75450.18551330.1592557X-RAY DIFFRACTION100
1.7545-1.78190.17491270.15492602X-RAY DIFFRACTION100
1.7819-1.81110.19811520.1562568X-RAY DIFFRACTION100
1.8111-1.84240.17861450.15992582X-RAY DIFFRACTION100
1.8424-1.87590.20481300.15682589X-RAY DIFFRACTION100
1.8759-1.91190.17211410.15872613X-RAY DIFFRACTION100
1.9119-1.9510.18061490.15992559X-RAY DIFFRACTION100
1.951-1.99340.19221260.15352597X-RAY DIFFRACTION100
1.9934-2.03980.18181390.15762595X-RAY DIFFRACTION100
2.0398-2.09080.20091570.15852567X-RAY DIFFRACTION100
2.0908-2.14730.19151480.15672602X-RAY DIFFRACTION100
2.1473-2.21050.16421440.15792597X-RAY DIFFRACTION100
2.2105-2.28180.19091480.15932597X-RAY DIFFRACTION100
2.2818-2.36340.18931300.15792640X-RAY DIFFRACTION100
2.3634-2.4580.19241140.1582618X-RAY DIFFRACTION100
2.458-2.56990.19581260.16122607X-RAY DIFFRACTION100
2.5699-2.70530.18971570.16892625X-RAY DIFFRACTION100
2.7053-2.87480.23061530.17192616X-RAY DIFFRACTION100
2.8748-3.09670.18341300.17152653X-RAY DIFFRACTION100
3.0967-3.40830.18911320.16072650X-RAY DIFFRACTION100
3.4083-3.90130.1521530.14712668X-RAY DIFFRACTION100
3.9013-4.91430.13891400.12752706X-RAY DIFFRACTION100
4.9143-46.38910.17821610.17372818X-RAY DIFFRACTION100

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