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- PDB-7o7t: Structure of the PL6 family alginate lyase Patl3640 from Pseudoal... -

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Basic information

Entry
Database: PDB / ID: 7o7t
TitleStructure of the PL6 family alginate lyase Patl3640 from Pseudoalteromonas atlantica T6c in complex with 4-deoxy-L-erythro-5-hexoseulose uronic acid
ComponentsPoly(Beta-D-mannuronate) lyase
KeywordsLYASE / beta helix / complex
Function / homologyPL-6 family / Chondroitinase B / mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / Pectin lyase fold / Pectin lyase fold/virulence factor / 4-deoxy-L-erythro-hex-5-ulosuronic acid / Poly(Beta-D-mannuronate) lyase
Function and homology information
Biological speciesPseudoalteromonas atlantica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 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)79,3056
Polymers78,8201
Non-polymers4845
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SAXS and gel filtration supports a dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint5 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.232, 78.232, 266.799
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 78820.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas atlantica (strain T6c / ATCC BAA-1087) (bacteria)
Strain: T6c / ATCC BAA-1087 / Gene: Patl_3640 / Plasmid: pFO4 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q15PP6, mannuronate-specific alginate lyase
#2: Chemical ChemComp-V4W / 4-deoxy-L-erythro-hex-5-ulosuronic acid / (4S,5S)-4,5-bis(oxidanyl)-2,6-bis(oxidanylidene)hexanoic acid / (4S,5S)-4,5-Dihydroxy-2,6-dioxohexanoic acid / 4-deoxy-L-erythro-5-hexoseulose uronic acid / 440352


Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Mg acetate, 0.1 M Na nitrate, 8% (w/v) PEG 10000, 0.15 mM CYMAL-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.05→47.53 Å / Num. obs: 60589 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.99 / Net I/σ(I): 18
Reflection shellResolution: 2.05→2.17 Å / Num. unique obs: 9328 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Patl3640 (PDB ID 7O77)

7o77


Resolution: 2.05→47.53 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 3007 4.97 %RANDOM
Rwork0.2091 57489 --
obs0.2108 60496 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.13 Å2 / Biso mean: 54.6482 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.05→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5398 0 32 261 5691
Biso mean--62.62 57.1 -
Num. residues----716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.080.40821210.36172629275098
2.08-2.120.34681300.314227692899100
2.12-2.160.36911670.315326312798100
2.16-2.20.32551230.306827352858100
2.2-2.240.33211560.292726752831100
2.24-2.290.30741430.272127082851100
2.29-2.350.27151740.249926432817100
2.35-2.410.26621540.23326862840100
2.41-2.470.25211070.236627522859100
2.47-2.540.27691460.232727132859100
2.54-2.630.25861410.21327172858100
2.63-2.720.26591390.208627232862100
2.72-2.830.25081410.205127082849100
2.83-2.960.24951390.219927312870100
2.96-3.110.25971580.215327282886100
3.11-3.310.23141430.206427472890100
3.31-3.560.24451360.196927982934100
3.56-3.920.23251450.197227742919100
3.92-4.490.18941320.175827842916100
4.49-5.650.22921710.180428282999100
5.65-47.530.23831410.21530103151100

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