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- PDB-7bwp: Crystal complex of endo-deglycosylated PcHNL5 with (R)-mandelonitrile -

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Basic information

Entry
Database: PDB / ID: 7bwp
TitleCrystal complex of endo-deglycosylated PcHNL5 with (R)-mandelonitrile
ComponentsPREDICTED: (R)-mandelonitrile lyase
KeywordsLYASE / Complex / endo-deglycosylated
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 / (2R)-hydroxy(phenyl)ethanenitrile / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / (R)-mandelonitrile lyase / (R)-mandelonitrile lyase 1
Similarity search - Component
Biological speciesPrunus dulcis (almond)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 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
DepositionApr 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.4Mar 5, 2025Group: Data collection / Database references / Category: citation / diffrn_detector
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_detector.detector

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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)61,63411
Polymers59,1871
Non-polymers2,44710
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint14 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.544, 91.095, 130.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 PREDICTED: (R)-mandelonitrile lyase


Mass: 59186.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prunus dulcis (almond) / Gene: ALMOND_2B028509 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A5E4GBK6, UniProt: O24243*PLUS
#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

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Non-polymers , 5 types, 452 molecules

#2: Chemical ChemComp-MXN / (2R)-hydroxy(phenyl)ethanenitrile / (R)-mandelonitrile


Mass: 133.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO / 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.48 Å3/Da / Density % sol: 50.44 %
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 - 8.5

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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 6M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 55236 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 17.76 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.057 / Net I/σ(I): 34.3
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 16.6 / Num. unique obs: 2751 / CC1/2: 0.978

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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: 1.802→46.305 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.98
RfactorNum. reflection% reflection
Rfree0.1968 2813 5.1 %
Rwork0.1599 --
obs0.1617 55103 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.49 Å2 / Biso mean: 19.2832 Å2 / Biso min: 7.31 Å2
Refinement stepCycle: final / Resolution: 1.802→46.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3971 0 159 448 4578
Biso mean--24.25 29.09 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064235
X-RAY DIFFRACTIONf_angle_d0.8635796
X-RAY DIFFRACTIONf_chiral_restr0.056665
X-RAY DIFFRACTIONf_plane_restr0.006743
X-RAY DIFFRACTIONf_dihedral_angle_d7.3062427
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8024-1.83350.23081500.2252897
1.8335-1.86680.24361570.18122529100
1.8668-1.90270.18421330.16992593100
1.9027-1.94160.22021090.17042606100
1.9416-1.98380.18921570.1612569100
1.9838-2.02990.22091520.16592564100
2.0299-2.08070.21291390.17032606100
2.0807-2.13690.2161320.16582587100
2.1369-2.19980.19481230.16792587100
2.1998-2.27080.20591410.1652622100
2.2708-2.3520.21131570.16242579100
2.352-2.44610.19871570.15992597100
2.4461-2.55750.20771460.1612594100
2.5575-2.69230.21661240.16072635100
2.6923-2.86090.20331360.1692623100
2.8609-3.08180.2351310.16832644100
3.0818-3.39180.18261330.15412660100
3.3918-3.88240.18011430.14472673100
3.8824-4.89060.16161400.1291268299
4.8906-100.18031530.1765281299

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