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- PDB-7o79: Structure of the PL6 family polysaccharide lyase Pedsa3628 from P... -

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Basic information

Entry
Database: PDB / ID: 7o79
TitleStructure of the PL6 family polysaccharide lyase Pedsa3628 from Pseudopedobacter saltans
ComponentsPoly(Beta-D-mannuronate) lyase
KeywordsLYASE / beta helix / polysaccharide lyase
Function / homology
Function and homology information


mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity
Similarity search - Function
PL-6 family / Chondroitinase B / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Poly(Beta-D-mannuronate) lyase
Similarity search - Component
Biological speciesPseudopedobacter saltans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsBallut, L. / Violot, S. / Carrique, L. / Aghajari, N.
CitationJournal: Glycobiology / Year: 2021
Title: Exploring molecular determinants of polysaccharide lyase family 6-1 enzyme activity.
Authors: Violot, S. / Galisson, F. / Carrique, L. / Jugnarain, V. / Conchou, L. / Robert, X. / Thureau, A. / Helbert, W. / Aghajari, N. / Ballut, L.
History
DepositionApr 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 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: Poly(Beta-D-mannuronate) lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0732
Polymers49,9781
Non-polymers951
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SAXS and gel filtration shows a dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-4 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.190, 51.746, 74.262
Angle α, β, γ (deg.)90.000, 97.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Poly(Beta-D-mannuronate) lyase


Mass: 49978.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first residue of the construct is not seen in the electron density
Source: (gene. exp.) Pseudopedobacter saltans (strain ATCC 51119 / DSM 12145 / JCM 21818 / LMG 10337 / NBRC 100064 / NCIMB 13643) (bacteria)
Strain: ATCC 51119 / DSM 12145 / JCM 21818 / LMG 10337 / NBRC 100064 / NCIMB 13643
Gene: Pedsa_3628 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F0S4Y3, mannuronate-specific alginate lyase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M K phosphate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.95372 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.93→48.49 Å / Num. obs: 32727 / % possible obs: 98.5 % / Redundancy: 6.6 % / CC1/2: 0.996 / Net I/σ(I): 8
Reflection shellResolution: 1.93→2.05 Å / Num. unique obs: 5026 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ITG

6itg


Resolution: 1.93→48.49 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2094 1594 4.87 %
Rwork0.1772 31110 -
obs0.1789 32704 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.73 Å2 / Biso mean: 29.5505 Å2 / Biso min: 15.9 Å2
Refinement stepCycle: final / Resolution: 1.93→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 5 344 3603
Biso mean--43.42 37.27 -
Num. residues----429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.93-20.32071280.26162586271491
2-2.070.271340.240428402974100
2.07-2.150.28431400.222528512991100
2.15-2.250.23421400.200828282968100
2.25-2.370.23861300.197128392969100
2.37-2.510.26141500.201228362986100
2.52-2.710.22611640.18728342998100
2.71-2.980.21931390.171828653004100
2.98-3.410.19371480.164128573005100
3.41-4.30.1721600.139628493009100
4.3-48.490.17721610.16622925308699

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