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- PDB-8rbr: Neutron structure of alginate lyase PsPL7C from Paradendryphiella... -

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Basic information

Entry
Database: PDB / ID: 8rbr
TitleNeutron structure of alginate lyase PsPL7C from Paradendryphiella salina
ComponentsAlginate lyase
KeywordsLYASE / alginate lyase / neutron structure / beta jelly-roll
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: 1.8 Å
AuthorsMeilleur, F. / Morth, J.P. / Wilkens, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Neutron structure of alginate lyase PsPL7C from Paradendryphiella salina
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


Theoretical massNumber of molelcules
Total (without water)25,5441
Polymers25,5441
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 area10060 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: 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: Water ChemComp-HOH / water / Water


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

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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: May 12, 2020
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 1.8→27.23 Å / Num. obs: 41523 / % possible obs: 84.03 % / Redundancy: 3.2 % / Biso Wilson estimate: 13.14 Å2 / CC1/2: 0.9 / Net I/σ(I): 5.29
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 705 / CC1/2: 0.32

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Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.23 Å / SU ML: 0.1456 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 14.8622
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1673 2082 5.01 %
Rwork0.1251 39441 -
obs0.1271 41523 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.01 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.01251831
NEUTRON DIFFRACTIONf_angle_d1.20682495
NEUTRON DIFFRACTIONf_chiral_restr0.0777280
NEUTRON DIFFRACTIONf_plane_restr0.0085399
NEUTRON DIFFRACTIONf_dihedral_angle_d13.6671645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.2071200.18332660NEUTRON DIFFRACTION100
1.84-1.890.18591330.15722644NEUTRON DIFFRACTION100
1.89-1.940.17921650.14252564NEUTRON DIFFRACTION100
1.94-20.15991510.12962655NEUTRON DIFFRACTION100
2-2.060.1709970.12852668NEUTRON DIFFRACTION100
2.06-2.130.18091440.13022599NEUTRON DIFFRACTION100
2.13-2.220.14641560.12372613NEUTRON DIFFRACTION100
2.22-2.320.17411430.12042631NEUTRON DIFFRACTION100
2.32-2.440.16931540.13152638NEUTRON DIFFRACTION100
2.44-2.60.18621720.13442584NEUTRON DIFFRACTION100
2.6-2.80.17291200.13192645NEUTRON DIFFRACTION100
2.8-3.080.17521250.14012651NEUTRON DIFFRACTION100
3.08-3.520.17971450.1172620NEUTRON DIFFRACTION100
3.52-4.430.12911340.09822629NEUTRON DIFFRACTION100
4.43-27.230.15591230.10952640NEUTRON DIFFRACTION99.6

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