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- PDB-8r43: Crystal structure of Paradendryphiella salina PL7C alginate lyase... -

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Basic information

Entry
Database: PDB / ID: 8r43
TitleCrystal structure of Paradendryphiella salina PL7C alginate lyase mutant H110N in complex with tri-mannuronic acid
ComponentsAlginate lyase
KeywordsLYASE / Alginate lyase. beta-jelly roll
Function / homologyAlginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase
Function and homology information
Biological speciesParadendryphiella salina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.87 Å
AuthorsWilkens, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Unraveling the molecular mechanism of polysaccharide lyases for efficient alginate degradation.
Authors: Rivas-Fernandez, J.P. / Vuillemin, M. / Pilgaard, B. / Klau, L.J. / Fredslund, F. / Lund-Hanssen, C. / Welner, D.H. / Meyer, A.S. / Morth, J.P. / Meilleur, F. / Aachmann, F.L. / Rovira, C. / Wilkens, C.
History
DepositionNov 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0903
Polymers25,5201
Non-polymers5692
Water7,404411
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint0 kcal/mol
Surface area9440 Å2
Unit cell
Length a, b, c (Å)77.060, 38.620, 74.630
Angle α, β, γ (deg.)90.000, 116.760, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-427-

HOH

21A-724-

HOH

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Components

#1: Protein Alginate lyase


Mass: 25520.199 Da / Num. of mol.: 1 / Mutation: H110N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paradendryphiella salina (fungus) / Gene: PsAlg7C / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A7I9C8Z1
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122A-1a_1-5][a1122A-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.94 Å3/Da / Density % sol: 36.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 30% PEG3350, 0.1M Bis-Tris pH 5.5, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.65 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 0.87→27.7 Å / Num. obs: 159325 / % possible obs: 99.31 % / Redundancy: 6.8 % / Biso Wilson estimate: 9.36 Å2 / CC1/2: 1 / Net I/σ(I): 14.39
Reflection shellResolution: 0.87→0.9 Å / Num. unique obs: 15618 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIXdev_4788refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.87→27.7 Å / SU ML: 0.1374 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.2374
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1409 2098 1.32 %
Rwork0.1197 157180 -
obs0.12 159278 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.03 Å2
Refinement stepCycle: LAST / Resolution: 0.87→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 38 411 2185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062110
X-RAY DIFFRACTIONf_angle_d1.04012931
X-RAY DIFFRACTIONf_chiral_restr0.0923335
X-RAY DIFFRACTIONf_plane_restr0.0102389
X-RAY DIFFRACTIONf_dihedral_angle_d13.4484793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.87-0.890.46781360.469210189X-RAY DIFFRACTION97.27
0.89-0.910.36461390.370210400X-RAY DIFFRACTION98.38
0.91-0.940.26481370.275710350X-RAY DIFFRACTION98.65
0.94-0.960.2151390.215210378X-RAY DIFFRACTION98.86
0.96-10.16771380.180310374X-RAY DIFFRACTION99.08
1-1.030.17621390.151310396X-RAY DIFFRACTION99.24
1.03-1.070.14621410.133810508X-RAY DIFFRACTION99.41
1.07-1.120.11451390.113210460X-RAY DIFFRACTION99.57
1.12-1.180.10591410.093910516X-RAY DIFFRACTION99.68
1.18-1.250.0961400.095510492X-RAY DIFFRACTION99.78
1.25-1.350.12951410.099910557X-RAY DIFFRACTION99.96
1.35-1.490.10871410.102310571X-RAY DIFFRACTION99.99
1.49-1.70.12761420.103910595X-RAY DIFFRACTION100
1.7-2.150.131420.110210628X-RAY DIFFRACTION99.96
2.15-27.70.14781430.112410766X-RAY DIFFRACTION99.78

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