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- PDB-8rbn: Neutron structure of alginate lysase PsPL7C from Paradendryphiell... -

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Basic information

Entry
Database: PDB / ID: 8rbn
TitleNeutron structure of alginate lysase PsPL7C from Paradendryphiella salina soaked with penta-mannuronic acid
ComponentsAlginate lyase
KeywordsLYASE / alginate lyase / neutron structure / mannuronic acid
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)
MethodNEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMeilleur, F. / Morth, J.P. / Wilkens, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Neutron structure of alginate lysase PsPL7C from Paradendryphiella salina soaked with penta-mannuronic acid
Authors: Meilleur, F. / Morth, J.P. / Wilkens, C.
History
DepositionDec 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: 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)26,4433
Polymers25,5441
Non-polymers8992
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint11 kcal/mol
Surface area9930 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: 25544.244 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 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 / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% PEG 1500; 0.1 M TBG buffer pH 4

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SPALLATION SOURCE / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 2-4
DetectorType: ORNL ANGER CAMERA / Detector: SCINTILLATION / Date: Oct 4, 2020
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 2.15→13.85 Å / Num. obs: 11082 / % possible obs: 84.03 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.71 Å2 / CC1/2: 0.9 / Net I/σ(I): 5.29
Reflection shellResolution: 2.15→2.26 Å / Num. unique obs: 1091 / CC1/2: 0.45

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Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→27.41 Å / SU ML: 0.1673 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.0672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1767 726 5.02 %
Rwork0.1288 13734 -
obs0.1312 14460 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.02 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0124239
NEUTRON DIFFRACTIONf_angle_d1.79827284
NEUTRON DIFFRACTIONf_chiral_restr0.0894300
NEUTRON DIFFRACTIONf_plane_restr0.0068847
NEUTRON DIFFRACTIONf_dihedral_angle_d19.77641082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.260.24451560.15412668NEUTRON DIFFRACTION99.93
2.26-2.490.20411510.152702NEUTRON DIFFRACTION100
2.49-2.850.1771060.15152743NEUTRON DIFFRACTION100
2.85-3.590.19141580.12962751NEUTRON DIFFRACTION100
3.59-27.410.13561550.10262870NEUTRON DIFFRACTION99.74

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