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

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Basic information

Entry
Database: PDB / ID: 8bxz
TitleCrystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F in complex with penta-mannuronic acid
ComponentsAlginate lyase
KeywordsLYASE / beta-jeely roll / alginate lyase / mannuronate
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: 1.2 Å
AuthorsWilkens, C.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Other government Denmark
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
DepositionDec 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: 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)26,5233
Polymers25,5281
Non-polymers9952
Water6,882382
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.230, 39.990, 42.720
Angle α, β, γ (deg.)74.740, 78.480, 69.510
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Alginate lyase


Mass: 25528.244 Da / Num. of mol.: 1
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)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 898.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122A-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.06 Å3/Da / Density % sol: 40.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2 M Ammonium sulfate; 0.1 Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.2→36.62 Å / Num. obs: 58658 / % possible obs: 92.1 % / Redundancy: 3.29 % / Biso Wilson estimate: 7.16 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.54
Reflection shellResolution: 1.2→1.27 Å / Num. unique obs: 9001 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBE3data collection
XDSdata reduction
XDSdata scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→36.62 Å / SU ML: 0.0736 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 12.5952
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1409 2096 3.58 %
Rwork0.1153 56465 -
obs0.1163 58561 92.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.06 Å2
Refinement stepCycle: LAST / Resolution: 1.2→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 66 382 2205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00672022
X-RAY DIFFRACTIONf_angle_d1.13462794
X-RAY DIFFRACTIONf_chiral_restr0.0941330
X-RAY DIFFRACTIONf_plane_restr0.0084364
X-RAY DIFFRACTIONf_dihedral_angle_d13.1731716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.16441300.12533535X-RAY DIFFRACTION85.99
1.23-1.260.13631320.11153594X-RAY DIFFRACTION87.94
1.26-1.290.141360.1123639X-RAY DIFFRACTION88.91
1.29-1.330.14581380.10793730X-RAY DIFFRACTION90.67
1.33-1.370.13671400.10493754X-RAY DIFFRACTION92.27
1.37-1.420.12681400.10043791X-RAY DIFFRACTION92.76
1.42-1.480.12751390.09663743X-RAY DIFFRACTION91.86
1.48-1.550.1231400.09513778X-RAY DIFFRACTION93.09
1.55-1.630.12161420.09743834X-RAY DIFFRACTION93.29
1.63-1.730.13551430.10453826X-RAY DIFFRACTION93.9
1.73-1.860.13561400.11113781X-RAY DIFFRACTION92.28
1.86-2.050.13361440.10733870X-RAY DIFFRACTION94.65
2.05-2.350.13181440.11123863X-RAY DIFFRACTION94.35
2.35-2.960.15271420.12933808X-RAY DIFFRACTION93.67
2.96-36.620.15791460.13563919X-RAY DIFFRACTION95.56

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