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- PDB-9g99: Joint neutron and x-ray structure of apo alginate lyase PsAlg7C -

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Basic information

Entry
Database: PDB / ID: 9g99
TitleJoint neutron and x-ray structure of apo alginate lyase PsAlg7C
ComponentsAlginate lyase
KeywordsLYASE / 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: 8RBR
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase


Theoretical massNumber of molelcules
Total (without water)26,7141
Polymers26,7141
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.577, 60.971, 91.308
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: 26713.744 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.7 %
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
22931N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SPALLATION SOURCEORNL Spallation Neutron Source MANDI12-4
ROTATING ANODERIGAKU21.54
Detector
TypeIDDetectorDate
ORNL ANGER CAMERA1SCINTILLATIONJun 1, 2021
DECTRIS EIGER R 4M2PIXELJun 3, 2021
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: 9G99

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allDiffraction-IDNet I/σ(I)
2.15-13.851108284.43.20.90.190.1115.29
1.8-27.232217499.9212.60.980.130.037220.7
Reflection shell

Rpim(I) all: 0.14

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.15-2.230.233.4810910.45185
1.8-1.860.446.0821680.94298

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Processing

Refinement

Biso mean: 20.04 Å2 / 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-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-ID
2.15-13.85NEUTRON DIFFRACTION0.3020.2320.23554939441110814.9584.451
1.8-27.23X-RAY DIFFRACTION0.1640.1210.1232082221745.0199.972
Refinement stepCycle: LAST / Resolution: 2.15→13.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1768 0 0 199 1967
Refine LS restraintsType: f_dihedral_angle_d / Dev ideal: 18.185 / Number: 1086
LS refinement shellResolution: 4.43→27.23 Å
RfactorNum. reflection% reflection
Rfree0.1503 123 -
Rwork0.107 2640 -
obs--99.6 %

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