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- PDB-8rbi: Crystal structure of Paradendryphiella salina PL7C alginate lyase... -

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Basic information

Entry
Database: PDB / ID: 8rbi
TitleCrystal structure of Paradendryphiella salina PL7C alginate lyase mutant H124
ComponentsAlginate lyase
KeywordsLYASE / alginate lyase
Function / homologyAlginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / DI(HYDROXYETHYL)ETHER / Alginate lyase
Function and homology information
Biological speciesParadendryphiella salina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsWilkens, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant H124
Authors: 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

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Assembly

Deposited unit
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6493
Polymers25,5201
Non-polymers1292
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-3 kcal/mol
Surface area9680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.520, 38.450, 74.010
Angle α, β, γ (deg.)90.000, 116.620, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

21A-419-

HOH

31A-659-

HOH

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Components

#1: Protein Alginate lyase


Mass: 25520.199 Da / Num. of mol.: 1 / Mutation: H124N
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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 30% PEG3350, 0.1M Bis-Tris pH 5.5, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.6525 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6525 Å / Relative weight: 1
ReflectionResolution: 0.98→33.52 Å / Num. obs: 213697 / % possible obs: 98.64 % / Redundancy: 6.8 % / Biso Wilson estimate: 11.89 Å2 / CC1/2: 1 / Net I/σ(I): 17.36
Reflection shellResolution: 0.98→1 Å / Num. unique obs: 6866 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
MxCuBE3data collection
PHENIXdev_4788refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.98→33.52 Å / SU ML: 0.1221 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 18.9501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1486 2223 1.04 %
Rwork0.1237 211474 -
obs0.1239 213697 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.83 Å2
Refinement stepCycle: LAST / Resolution: 0.98→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1746 0 8 347 2101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641950
X-RAY DIFFRACTIONf_angle_d1.15022682
X-RAY DIFFRACTIONf_chiral_restr0.1019299
X-RAY DIFFRACTIONf_plane_restr0.0102351
X-RAY DIFFRACTIONf_dihedral_angle_d13.9583715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-10.39861390.357113215X-RAY DIFFRACTION98.45
1-1.020.31361380.29413234X-RAY DIFFRACTION98.72
1.02-1.050.23851380.242413186X-RAY DIFFRACTION98.84
1.05-1.080.24161400.216513317X-RAY DIFFRACTION98.69
1.08-1.110.22121380.191313173X-RAY DIFFRACTION98.89
1.11-1.150.14911400.14513263X-RAY DIFFRACTION98.88
1.15-1.190.14441390.135313331X-RAY DIFFRACTION98.91
1.19-1.230.16941420.124913195X-RAY DIFFRACTION98.61
1.23-1.290.15611340.121413196X-RAY DIFFRACTION98.73
1.29-1.360.11651420.11213230X-RAY DIFFRACTION98.96
1.36-1.440.13681430.112613248X-RAY DIFFRACTION98.68
1.44-1.560.13581390.100113157X-RAY DIFFRACTION98.75
1.56-1.710.11971350.123313291X-RAY DIFFRACTION98.58
1.71-1.960.14741330.117113157X-RAY DIFFRACTION98.28
1.96-2.470.13161400.115113138X-RAY DIFFRACTION98.07
2.47-33.520.14941430.112713143X-RAY DIFFRACTION98.08

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