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- PDB-8p6o: Crystal structure of Paradendryphiella salina PL7C alginate lyase... -

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Basic information

Entry
Database: PDB / ID: 8p6o
TitleCrystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F in complex with di-mannuronic acid
ComponentsAlginate lyase
KeywordsLYASE / beta-jelly roll / alginate lyase / complex
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsWilkens, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Paradendryphiella salina PL7C alginate lyase mutant Y220F in complex with di-mannuronic acid
Authors: Wilkens, C.
History
DepositionMay 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)26,3654
Polymers25,5281
Non-polymers8373
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-3 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.920, 39.880, 42.550
Angle α, β, γ (deg.)73.920, 77.080, 69.850
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Alginate lyase


Mass: 25528.244 Da / Num. of mol.: 1 / Mutation: Y220F
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 beta-D-mannopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 370.263 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122A-1a_1-5][a1122A-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-ManpA]{[(4+1)][b-D-ManpA]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 370.263 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122A-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2 M Ammonium sulfate; 0.1 Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.05→40.47 Å / Num. obs: 84336 / % possible obs: 90.6 % / Redundancy: 3.12 % / Biso Wilson estimate: 8.08 Å2 / CC1/2: 0.99 / Net I/σ(I): 5.84
Reflection shellResolution: 1.05→1.11 Å / Num. unique obs: 12463 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBE3data collection
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→40.47 Å / SU ML: 0.0828 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 13.5769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1395 2100 2.49 %
Rwork0.1161 82216 -
obs0.1167 84316 90.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.33 Å2
Refinement stepCycle: LAST / Resolution: 1.05→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 55 377 2179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00632011
X-RAY DIFFRACTIONf_angle_d1.06522785
X-RAY DIFFRACTIONf_chiral_restr0.0925330
X-RAY DIFFRACTIONf_plane_restr0.0085360
X-RAY DIFFRACTIONf_dihedral_angle_d13.7141721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.070.22791150.20864537X-RAY DIFFRACTION75.1
1.07-1.10.18911360.17935290X-RAY DIFFRACTION87.29
1.1-1.130.17691370.14765391X-RAY DIFFRACTION89.2
1.13-1.160.1661350.13515268X-RAY DIFFRACTION87.38
1.16-1.20.17141380.11845389X-RAY DIFFRACTION88.69
1.2-1.240.14151360.11585361X-RAY DIFFRACTION88.86
1.24-1.290.141390.11055433X-RAY DIFFRACTION89.7
1.29-1.350.13551410.1085502X-RAY DIFFRACTION91.41
1.35-1.430.13361450.10485679X-RAY DIFFRACTION93.24
1.43-1.510.12791440.10095643X-RAY DIFFRACTION93.58
1.51-1.630.13271440.09995625X-RAY DIFFRACTION93.39
1.63-1.80.1241470.1075754X-RAY DIFFRACTION94.92
1.8-2.060.14011460.1065739X-RAY DIFFRACTION95.21
2.06-2.590.14111470.11325737X-RAY DIFFRACTION94.86
2.59-40.470.12571500.1175868X-RAY DIFFRACTION96.97

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