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- PDB-7p90: Crystal structure of Paradendryphiella salina PL7A alginate lyase... -

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Basic information

Entry
Database: PDB / ID: 7p90
TitleCrystal structure of Paradendryphiella salina PL7A alginate lyase in complex with tetra-mannuronic acid products
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: 1.87 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 in complex with tetra-mannuronic acid products
Authors: Fredslund, F. / Welner, D.H. / Wilkens, C.
History
DepositionJul 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 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 13, 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

Downloads & links

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Assembly

Deposited unit
A: Alginate lyase (PL7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5433
Polymers25,4691
Non-polymers1,0752
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint16 kcal/mol
Surface area9270 Å2
Unit cell
Length a, b, c (Å)35.160, 80.920, 81.540
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 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 528.372 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a1122A-1b_1-5][a11eEA-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-4-deoxy-ManpA]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 546.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpAb1-4DManpAb1-4DManpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122A-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-ManpA]{[(4+1)][b-D-ManpA]{[(4+1)][b-D-ManpA]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
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: 0.953798 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953798 Å / Relative weight: 1
ReflectionResolution: 1.87→40.46 Å / Num. obs: 19676 / % possible obs: 98.4 % / Redundancy: 12.72 % / Biso Wilson estimate: 35.25 Å2 / CC1/2: 1 / Net I/σ(I): 24.74
Reflection shellResolution: 1.87→1.98 Å / Num. unique obs: 2869 / CC1/2: 0.94

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Processing

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

7ncz


Resolution: 1.87→36.41 Å / SU ML: 0.2074 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.9231
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 983 5 %
Rwork0.1671 18669 -
obs0.1692 19652 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.52 Å2
Refinement stepCycle: LAST / Resolution: 1.87→36.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 73 134 1949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00931884
X-RAY DIFFRACTIONf_angle_d1.11662579
X-RAY DIFFRACTIONf_chiral_restr0.0624323
X-RAY DIFFRACTIONf_plane_restr0.008326
X-RAY DIFFRACTIONf_dihedral_angle_d18.5421633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.970.30331250.25122374X-RAY DIFFRACTION89.06
1.97-2.090.27141390.22646X-RAY DIFFRACTION99.46
2.09-2.250.27991400.18152661X-RAY DIFFRACTION99.72
2.25-2.480.2181410.17962682X-RAY DIFFRACTION99.86
2.48-2.840.24811420.19462698X-RAY DIFFRACTION99.75
2.84-3.570.2421450.17442740X-RAY DIFFRACTION99.93
3.57-36.410.15851510.14162868X-RAY DIFFRACTION99.97
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)
12.39751669845-0.9961701491482.073114507945.40749298088-3.000591563467.48644809112-0.1128466782880.2401397139620.0497821142659-0.310211683990.0721941370376-0.3141649518620.3841625236580.354486928350.05258637020860.3090112905630.01606681791590.03344298682830.30837626058-0.05466225277260.3333527247634.2524087804412.87574318265.26860606925
21.771361517830.5419545034850.8777850777764.221940531661.07193476983.51833646425-0.0158847105056-0.1385806423070.0600045483690.428429505920.0605513605144-0.124449506065-0.00573913104621-0.0608880298329-0.01240696644520.2711152064460.0196296497294-0.02339032088580.2912530988810.001332304687840.2771783034551.0189055732823.336948321820.7839257836
32.891820318971.29704499225-1.8163994522.651613962490.8899152956263.85208343337-0.31776363345-0.1501002899210.06447131724290.144653659520.341498547047-0.116566686101-0.039803958404-0.1849244682850.01122715464560.3393844664170.0101152420061-0.1202565570920.19548803904-0.06505000341040.3586804316492.0693195850115.909654143717.4391353656
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 63 )0 - 631 - 42
22chain 'A' and (resid 64 through 223 )64 - 22343 - 202
33chain 'A' and (resid 224 through 247 )224 - 247203 - 226

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