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- PDB-7o84: Structure of the PL6 family alginate lyase Pedsa0632 from Pseudop... -

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Basic information

Entry
Database: PDB / ID: 7o84
TitleStructure of the PL6 family alginate lyase Pedsa0632 from Pseudopedobacter saltans in complex with substrate
ComponentsAlginate lyase
KeywordsLYASE / beta helix
Function / homologyPL-6 family / Chondroitinase B / Parallel beta-helix repeat / Parallel beta-helix repeats / Pectin lyase fold / Pectin lyase fold/virulence factor / Alginate lyase
Function and homology information
Biological speciesPseudopedobacter saltans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.177 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 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Data collection / Database references
Category: citation / database_2 / pdbx_entity_branch_descriptor
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 1.2May 1, 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

Downloads & links

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Assembly

Deposited unit
A: Alginate lyase
B: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1334
Polymers94,9002
Non-polymers1,2332
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint21 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.182, 47.583, 116.200
Angle α, β, γ (deg.)90.000, 98.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alginate lyase


Mass: 47450.051 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_0632 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F0S7Y7
#2: Polysaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic 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/[a1121A-1a_1-5][a11eEA-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][b-D-4-deoxy-ManpA]{}}}LINUCSPDB-CARE
#3: Polysaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L- ...4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 704.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a1121A-1a_1-5][a11eEA-1a_1-5]/1-1-1-2/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][a-L-GulpA]{[(4+1)][b-D-4-deoxy-ManpA]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Amm chloride, 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: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.17→47.58 Å / Num. obs: 46036 / % possible obs: 97.8 % / Redundancy: 3.3 % / CC1/2: 0.99 / Net I/σ(I): 4.8
Reflection shellResolution: 2.17→2.31 Å / Num. unique obs: 7197 / CC1/2: 0.43

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (29-NOV-2019)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: native Pedsa0632

Resolution: 2.177→43.97 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.874 / SU R Cruickshank DPI: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.305 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2862 2282 4.98 %RANDOM
Rwork0.2284 ---
obs0.2312 45831 98.3 %-
Displacement parametersBiso max: 78.09 Å2 / Biso mean: 40.9879 Å2 / Biso min: 21.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.0576 Å20 Å2-1.9927 Å2
2---8.1966 Å20 Å2
3---7.139 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.177→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 84 372 6749
Biso mean--64.43 41.37 -
Num. residues----817
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2231SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1139HARMONIC5
X-RAY DIFFRACTIONt_it6520HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion877SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5489SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6520HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg8849HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.49
X-RAY DIFFRACTIONt_other_torsion18.71
LS refinement shellResolution: 2.18→2.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2619 52 5.67 %
Rwork0.2257 865 -
all0.2278 917 -
obs--72.37 %

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