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- PDB-7ncz: Crystal structure of Paradendryphiella salina PL7A alginate lyase... -

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Basic information

Entry
Database: PDB / ID: 7ncz
TitleCrystal structure of Paradendryphiella salina PL7A alginate lyase mutant Y223F in complex with hexa-mannuronic acid
ComponentsAlginate lyase (PL7)
KeywordsLYASE / complex / beta jelly roll / mutant / alginate lyase
Function / homologyAlginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase (PL7)
Function and homology information
Biological speciesParadendryphiella salina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsFredslund, F. / Welner, D.H. / Wilkens, C.
Funding support Denmark, 1items
OrganizationGrant numberCountry
European Union (EU)9082-00021B Denmark
CitationJournal: To Be Published
Title: Crystal structure of Paradendryphiella salina PL7A alginate lyase mutant Y223F in complex with hexa-mannuronic acid
Authors: Fredslund, F. / Welner, D.H. / Wilkens, C.
History
DepositionJan 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase (PL7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9133
Polymers25,4531
Non-polymers1,4602
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint17 kcal/mol
Surface area9620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.810, 80.900, 81.210
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 (PL7)


Mass: 25452.715 Da / Num. of mol.: 1 / Mutation: Y223F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paradendryphiella salina (fungus) / Gene: PsAlg7A / Production host: Komagataella pastoris (fungus)
References: UniProt: A0A485PVH1, mannuronate-specific alginate lyase
#2: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid- ...beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 1250.882 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a1122A-1b_1-5]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% PEG 1500 and 0.1 M TBG buffer pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.64→40.6 Å / Num. obs: 53721 / % possible obs: 98.6 % / Redundancy: 6.96 % / Biso Wilson estimate: 22.33 Å2 / CC1/2: 1 / Net I/σ(I): 10.36
Reflection shellResolution: 1.64→1.73 Å / Num. unique obs: 8113 / CC1/2: 0.46 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YWF

6ywf


Resolution: 1.64→40.6 Å / SU ML: 0.1849 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.9321
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.19 2679 4.99 %
Rwork0.1524 50972 -
obs0.1542 53651 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 1.64→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 99 234 2084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861934
X-RAY DIFFRACTIONf_angle_d1.18372657
X-RAY DIFFRACTIONf_chiral_restr0.068329
X-RAY DIFFRACTIONf_plane_restr0.0064334
X-RAY DIFFRACTIONf_dihedral_angle_d8.5903258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.670.41941050.3272018X-RAY DIFFRACTION72.58
1.67-1.70.28671450.27272671X-RAY DIFFRACTION100
1.7-1.740.28261470.25682744X-RAY DIFFRACTION100
1.74-1.770.25851450.23322674X-RAY DIFFRACTION100
1.77-1.810.23971400.22182761X-RAY DIFFRACTION100
1.81-1.860.25021430.20372699X-RAY DIFFRACTION100
1.86-1.910.18231470.18082728X-RAY DIFFRACTION100
1.91-1.970.1961390.15782747X-RAY DIFFRACTION99.97
1.97-2.030.17811370.15022708X-RAY DIFFRACTION99.96
2.03-2.10.18581460.1482728X-RAY DIFFRACTION100
2.1-2.190.16361410.13882734X-RAY DIFFRACTION100
2.19-2.290.18711370.13722706X-RAY DIFFRACTION100
2.29-2.410.1661430.13352713X-RAY DIFFRACTION100
2.41-2.560.22091440.14122727X-RAY DIFFRACTION100
2.56-2.750.19771420.13772729X-RAY DIFFRACTION100
2.75-3.030.19191460.15262719X-RAY DIFFRACTION100
3.03-3.470.17661420.14412730X-RAY DIFFRACTION99.97
3.47-4.370.16611450.13232722X-RAY DIFFRACTION100
4.37-40.60.17321450.14112714X-RAY DIFFRACTION99.93

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