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- PDB-7nl3: Crystal structure of Paradendryphiella salina PL7A alginate lyase... -

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Basic information

Entry
Database: PDB / ID: 7nl3
TitleCrystal structure of Paradendryphiella salina PL7A alginate lyase mutant Y223F
ComponentsAlginate lyase (PL7)
KeywordsLYASE / complex / beta jelly roll / mutant / alginate lyase
Function / homologyAlginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase (PL7)
Function and homology information
Biological speciesParadendryphiella salina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFredslund, F. / Welner, D.H. / Wilkens, C.
Funding support Denmark, 1items
OrganizationGrant numberCountry
European Union (EU)9082-00021B 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
DepositionFeb 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Jul 2, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase (PL7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6622
Polymers25,4531
Non-polymers2091
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint2 kcal/mol
Surface area9890 Å2
Unit cell
Length a, b, c (Å)34.780, 80.620, 80.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Alginate lyase (PL7)


Mass: 25452.715 Da / Num. of mol.: 1 / Mutation: Y223F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paradendryphiella salina (fungus) / Gene: PsAlg7A / Production host: Komagataella pastoris (fungus)
References: UniProt: A0A485PVH1, mannuronate-specific alginate lyase
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% PEG 1500 and 0.1 M TBG buffer pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→40.43 Å / Num. obs: 331071 / % possible obs: 99.4 % / Redundancy: 6.93 % / Biso Wilson estimate: 25.39 Å2 / CC1/2: 1 / Net I/σ(I): 9.19
Reflection shellResolution: 1.7→1.81 Å / Num. unique obs: 50389 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
MxCuBE1.18.2_3874data collection
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NCZ

7ncz


Resolution: 1.7→40.43 Å / SU ML: 0.2083 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.8886
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1931 2384 4.99 %
Rwork0.1529 45409 -
obs0.1549 47793 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.85 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 14 216 1981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881843
X-RAY DIFFRACTIONf_angle_d1.07162518
X-RAY DIFFRACTIONf_chiral_restr0.0658294
X-RAY DIFFRACTIONf_plane_restr0.0065327
X-RAY DIFFRACTIONf_dihedral_angle_d8.9882258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.35351340.31232484X-RAY DIFFRACTION91.12
1.74-1.780.3211430.29352633X-RAY DIFFRACTION100
1.78-1.820.30391350.25822709X-RAY DIFFRACTION100
1.82-1.860.28311430.23482695X-RAY DIFFRACTION100
1.86-1.910.23571480.20952697X-RAY DIFFRACTION100
1.91-1.970.21041320.18362680X-RAY DIFFRACTION100
1.97-2.030.17651370.17472675X-RAY DIFFRACTION99.96
2.03-2.110.22531400.16582662X-RAY DIFFRACTION100
2.11-2.190.19991380.15352727X-RAY DIFFRACTION100
2.19-2.290.20751380.13492667X-RAY DIFFRACTION100
2.29-2.410.15391420.13322656X-RAY DIFFRACTION99.96
2.41-2.560.19981440.13752686X-RAY DIFFRACTION100
2.56-2.760.1971400.14012718X-RAY DIFFRACTION99.93
2.76-3.040.18631420.15492679X-RAY DIFFRACTION99.93
3.04-3.480.16641420.14082689X-RAY DIFFRACTION99.86
3.48-4.380.15781410.12832676X-RAY DIFFRACTION100
4.38-40.430.19231450.13872676X-RAY DIFFRACTION99.86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.24388485472-0.03791190492810.6887549717564.13694923547-0.7740520487594.29874728856-0.05209345433190.108164895841-0.0469605680608-0.1792465137810.0475848704511-0.167844774510.2172251399420.2896556333020.02045846037280.1598239286120.0217227263440.0197799122390.138824901245-0.01741866544390.1227299743954.3826968882212.63747155754.9924509904
21.353757573880.09689308340590.3685896169721.692352407750.03448252086891.67096314763-0.0280056043426-0.1503215898980.08431112811170.1245755352190.0106251750173-0.0111331353406-0.0572794652255-0.0386165290020.01678954190470.185015078521-0.00308747366288-0.00760772629930.207704690512-0.003193201804450.2156318799041.6463767832121.995826199821.0874894375
33.09364405534-1.98391922363-0.3297967549066.52038452745-0.6467365689221.77987163735-0.119337558234-0.1411316391930.258136636403-0.1702013609380.164311137610.336477441728-0.253049209702-0.462415686629-0.03183444903550.2331182523750.00687782008321-0.03793544765980.171021260626-0.0226063334240.217888824229-4.2552362719218.155656866913.1696063066
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 63 )0 - 631 - 42
22chain 'A' and (resid 64 through 232 )64 - 23243 - 222
33chain 'A' and (resid 233 through 248 )233 - 248223 - 241

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