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

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Basic information

Entry
Database: PDB / ID: 7pbf
TitleCrystal structure of Paradendryphiella salina PL7A alginate lyase in complex with di-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: 1.54 Å
AuthorsFredslund, F. / Welner, D.H. / Wilkens, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)9082-00021BEuropean Union
CitationJournal: To Be Published
Title: Crystal structure of Paradendryphiella salina PL7A alginate lyase in complex with di-mannuronic acid
Authors: Fredslund, F. / Welner, D.H. / Wilkens, C.
History
DepositionAug 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 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

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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)25,8392
Polymers25,4691
Non-polymers3701
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint5 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.000, 80.640, 81.190
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: 25468.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paradendryphiella salina (fungus) / Gene: PsAlg7A / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A485PVH1
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
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: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.54→40.32 Å / Num. obs: 34390 / % possible obs: 99.5 % / Redundancy: 12.89 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 1 / Net I/σ(I): 18.68
Reflection shellResolution: 1.54→1.64 Å / Num. unique obs: 5324 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBE3data collection
XDSdata reduction
XDSdata scaling
Coot0.9.4model building
PHASER1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NCZ

7ncz


Resolution: 1.54→40.32 Å / SU ML: 0.2054 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.1641
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195 1720 5.01 %
Rwork0.1707 32619 -
obs0.1719 34339 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.41 Å2
Refinement stepCycle: LAST / Resolution: 1.54→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 25 117 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851850
X-RAY DIFFRACTIONf_angle_d0.97912535
X-RAY DIFFRACTIONf_chiral_restr0.0612305
X-RAY DIFFRACTIONf_plane_restr0.007328
X-RAY DIFFRACTIONf_dihedral_angle_d13.4369641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.590.4021330.38222515X-RAY DIFFRACTION93.8
1.59-1.640.33611420.28772690X-RAY DIFFRACTION99.82
1.64-1.70.29711420.26172694X-RAY DIFFRACTION99.79
1.7-1.770.27061420.22732692X-RAY DIFFRACTION99.82
1.77-1.850.25651430.21642709X-RAY DIFFRACTION99.79
1.85-1.950.22131420.18172699X-RAY DIFFRACTION99.96
1.95-2.070.22621430.1712708X-RAY DIFFRACTION99.86
2.07-2.230.19881420.16812698X-RAY DIFFRACTION99.89
2.23-2.450.18761450.16452745X-RAY DIFFRACTION99.9
2.45-2.810.20071440.17082740X-RAY DIFFRACTION99.97
2.81-3.530.20471480.17372810X-RAY DIFFRACTION100
3.54-40.320.14821540.14192919X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.93027630185-0.1784394965360.8829347043024.87570737349-1.608869336274.55645792216-0.09786162824760.05922633835190.00683225234915-0.326157298570.0678109691653-0.2463720814960.2751374402970.2047386404210.009655554677960.2186885189470.02449875737490.02415876448270.182266344591-0.02815252143330.1799120480974.1861794981412.83959036155.15838915311
21.398117203630.2096362547170.3498142026493.050268089190.4000028330522.8272761255-0.0254597600641-0.1674502886330.02917542845590.3871135838640.073128445747-0.137357775725-0.009201615318030.0100197752239-0.02863861147370.2186832680840.0175372476656-0.0248650753070.22343732627-0.0047500294660.2217217587981.8104975447822.431717852921.1338012194
31.617903722330.717526723386-1.790586051552.798227112810.7963484070733.0171529042-0.1693042723550.02545479791020.4772590844720.1285756491150.0762059070355-0.0151250079435-0.355289981156-0.1756979456780.07891336521820.312409944645-0.0146531419079-0.1130873347030.172956530858-0.009587401844020.389732468133-1.711539433419.266067626415.3667693782
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 63 )A0 - 631 - 42
22chain 'A' and (resid 64 through 232 )A64 - 23243 - 211
33chain 'A' and (resid 233 through 247 )A - C233 - 306212

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