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- PDB-7o7a: Structure of the PL6 family alginate lyase Pedsa0632 from Pseudop... -

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Basic information

Entry
Database: PDB / ID: 7o7a
TitleStructure of the PL6 family alginate lyase Pedsa0632 from Pseudopedobacter saltans
ComponentsAliginate lyase
KeywordsLYASE / beta helix
Function / homology
Function and homology information


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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta
Similarity search - Domain/homology
Poly(Beta-D-mannuronate) lyase
Similarity search - Component
Biological speciesPseudopedobacter saltans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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: Aliginate lyase
B: Aliginate lyase


Theoretical massNumber of molelcules
Total (without water)95,1942
Polymers95,1942
Non-polymers00
Water10,989610
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint3 kcal/mol
Surface area30090 Å2
Unit cell
Length a, b, c (Å)81.290, 47.290, 116.730
Angle α, β, γ (deg.)90.000, 98.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aliginate lyase


Mass: 47597.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: first 14 residues of construct 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_0632 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F0S7Y7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M K sulfate, 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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.99→80.49 Å / Num. obs: 58008 / % possible obs: 94.7 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 11.7
Reflection shellResolution: 1.99→2.04 Å / Num. unique obs: 4451 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (29-NOV-2019)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ITG

6itg


Resolution: 1.99→57.79 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.213 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 2814 4.86 %RANDOM
Rwork0.2102 ---
obs0.2119 57894 94.5 %-
Displacement parametersBiso max: 86.51 Å2 / Biso mean: 33.19 Å2 / Biso min: 16.26 Å2
Baniso -1Baniso -2Baniso -3
1-6.1056 Å20 Å2-4.2134 Å2
2---12.8731 Å20 Å2
3---6.7674 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: final / Resolution: 1.99→57.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 0 610 6880
Biso mean---42.77 -
Num. residues----814
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2189SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1133HARMONIC5
X-RAY DIFFRACTIONt_it6428HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion853SEMIHARMONIC5
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_contact5705SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6428HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg8733HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion17.02
LS refinement shellResolution: 1.99→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2569 44 3.8 %
Rwork0.2309 1114 -
all0.2318 1158 -
obs--98.62 %

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