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- PDB-9g98: Joint neutron and x-ray structure of alginate lyase PsAlg7C soake... -

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Basic information

Entry
Database: PDB / ID: 9g98
TitleJoint neutron and x-ray structure of alginate lyase PsAlg7C soaked with pentamannuronic acid
ComponentsAlginate lyase
KeywordsLYASE / alginate lyase / complex / beta jellyroll / alginate
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 / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWilkens, C. / Meilleur, F. / Morth, J.P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
DanScatt 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
DepositionJul 24, 2024Deposition site: PDBE / Processing site: PDBE
SupersessionJul 30, 2025ID: 8RBN
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0373
Polymers25,1391
Non-polymers8992
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint11 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.089, 61.451, 91.882
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


Mass: 25138.834 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 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 352.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a1122A-1b_1-5][a11eEA-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-4-deoxy-ManpA]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


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


Mass: 18.015 Da / Num. of mol.: 124 / 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

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.3347.12
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG3350,0.1M Bis-Tris pH 5.5, 0.3M NaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22932N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SPALLATION SOURCEORNL Spallation Neutron Source MANDI12-4
ROTATING ANODERIGAKU MICROMAX-007 HF21.54
Detector
TypeIDDetectorDate
ORNL ANGER CAMERA1SCINTILLATIONJul 12, 2022
DECTRIS EIGER R 4M2PIXELJul 15, 2022
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
31.541
Reflection

Entry-ID: 9G98

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2.15-14.571277294.614.70.940.220.118.2
2.1-27.42145131006.30.990.120.05212.4
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allDiffraction-ID
2.15-2.220.273.311810.270.141
2.1-2.160.66411470.80.292

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Processing

Refinement

Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-ID
2.15-14.57NEUTRON DIFFRACTION19.740.27670.23490.237163213734127604.9594.761
2.1-27.41X-RAY DIFFRACTION0.17450.12790.1303726144605.0299.932
Refinement stepCycle: LAST / Resolution: 2.15→14.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 61 124 1953
Refine LS restraintsType: f_bond_d / Dev ideal: 0.0129 / Number: 4148
LS refinement shellResolution: 2.1→2.26 Å
RfactorNum. reflection% reflection
Rfree0.2339 156 -
Rwork0.1522 2668 -
obs--99.93 %

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