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- PDB-7o78: Structure of the PL6 family chondroitinase B from Pseudopedobacte... -

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Basic information

Entry
Database: PDB / ID: 7o78
TitleStructure of the PL6 family chondroitinase B from Pseudopedobacter saltans, Pedsa3807
ComponentsPolysaccharide lyase from Pseudopedobacter saltans, Pedsa3807
KeywordsLYASE / beta helix
Function / homologyPL-6 family / Chondroitinase B / Pectin lyase fold / Pectin lyase fold/virulence factor / Uncharacterized protein
Function and homology information
Biological speciesPseudopedobacter saltans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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: Polysaccharide lyase from Pseudopedobacter saltans, Pedsa3807
B: Polysaccharide lyase from Pseudopedobacter saltans, Pedsa3807


Theoretical massNumber of molelcules
Total (without water)110,9622
Polymers110,9622
Non-polymers00
Water16,358908
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, SAXS and gel filtration indicate a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint5 kcal/mol
Surface area35980 Å2
Unit cell
Length a, b, c (Å)78.330, 87.450, 148.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polysaccharide lyase from Pseudopedobacter saltans, Pedsa3807


Mass: 55481.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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_3807 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F0S763
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M tri-Li citrate, 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: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.58→75.36 Å / Num. obs: 135111 / % possible obs: 96 % / Redundancy: 13 % / CC1/2: 1 / Net I/σ(I): 19.4
Reflection shellResolution: 1.58→1.62 Å / Num. unique obs: 10276 / CC1/2: 0.844

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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: 1OFM

1ofm


Resolution: 1.58→58.35 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.88 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2102 6756 5 %
Rwork0.1785 128252 -
obs0.1802 135008 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.81 Å2 / Biso mean: 24.5804 Å2 / Biso min: 12.03 Å2
Refinement stepCycle: final / Resolution: 1.58→58.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7617 0 0 908 8525
Biso mean---35.53 -
Num. residues----983
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.60.26222450.24634408465399
1.6-1.610.27812290.24764356458599
1.61-1.630.30892190.24674382460199
1.63-1.650.25052540.234943664620100
1.65-1.680.28382450.218744314676100
1.68-1.70.25192220.219543864608100
1.7-1.720.26492290.216244094638100
1.72-1.750.25962450.209344124657100
1.75-1.780.22912390.206943944633100
1.78-1.810.2452080.203244294637100
1.81-1.840.25172250.203844094634100
1.84-1.870.22622340.196143794613100
1.87-1.910.24812520.19194385463799
1.91-1.940.25121120.21572027213946
1.94-1.990.21862270.178344224649100
1.99-2.030.2232320.173744404672100
2.03-2.080.20481780.17383687386583
2.08-2.140.20732190.176944554674100
2.14-2.20.19822790.172644024681100
2.2-2.270.21962040.17423871407588
2.27-2.360.22231960.17945084704100
2.36-2.450.22422040.1834471467599
2.45-2.560.20742280.176344434671100
2.56-2.70.20921940.17433874406886
2.7-2.870.18321990.169844974696100
2.87-3.090.192500.169344724722100
3.09-3.40.20942170.170145224739100
3.4-3.870.1952510.15643916416791
3.91-4.90.16872640.14954372463699
4.9-58.350.22672560.19474727498399

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