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- PDB-7bjt: Structure-function analysis of a new PL17 oligoalginate lyase fro... -

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Basic information

Entry
Database: PDB / ID: 7bjt
TitleStructure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium Zobellia galactanivorans DsijT
ComponentsAlginate lyase, family PL17
KeywordsHYDROLASE / alginate lyase / delta-guluronate complex / family PL17 / exo-acting marine enzyme
Function / homology
Function and homology information


mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / periplasmic space / metal ion binding
Similarity search - Function
Beta-galactosidase; Chain A, domain 5 - #70 / Heparinase II/III-like / Heparinase II/III-like, C-terminal / Alginate lyase domain / Alginate lyase / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase / Alpha/alpha barrel ...Beta-galactosidase; Chain A, domain 5 - #70 / Heparinase II/III-like / Heparinase II/III-like, C-terminal / Alginate lyase domain / Alginate lyase / Chondroitin AC/alginate lyase / Chondroitin AC/alginate lyase / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
D-MALATE / Alginate lyase, family PL17
Similarity search - Component
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsCzjzek, M. / Roret, T. / Jouanneau, D. / Le Duff, N. / Jeudy, A.
Funding support France, European Union, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-10-BTBR-04 France
European CommissionFP7-NMP, project 604530European Union
CitationJournal: Glycobiology / Year: 2021
Title: Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium Zobellia galactanivorans DsijT.
Authors: Jouanneau, D. / Klau, L.J. / Larocque, R. / Jaffrennou, A. / Duval, G. / Le Duff, N. / Roret, T. / Jeudy, A. / Aachmann, F.L. / Czjzek, M. / Thomas, F.
History
DepositionJan 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _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

Downloads & links

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Assembly

Deposited unit
A: Alginate lyase, family PL17
B: Alginate lyase, family PL17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,06514
Polymers170,3032
Non-polymers76212
Water23,8881326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The enzyme is a dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-96 kcal/mol
Surface area49270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.390, 163.390, 166.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alginate lyase, family PL17


Mass: 85151.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zobellia galactanivorans (strain DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij) (bacteria)
Strain: DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij
Gene: alyA3, zobellia_2624 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G0LCA3, mannuronate-specific alginate lyase

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Non-polymers , 5 types, 1338 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1326 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.91 Å3/Da / Density % sol: 68.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: protein solution of 11.3 mg.ml-1 concentration. Drops of 2 micro-l volume of this protein solution were mixed with 1 micro-l of crystallization solution that contained 2.1 M DL-Malic acid pH ...Details: protein solution of 11.3 mg.ml-1 concentration. Drops of 2 micro-l volume of this protein solution were mixed with 1 micro-l of crystallization solution that contained 2.1 M DL-Malic acid pH 7.0, and equilibrated against a reservoir containing 500 micro-l.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 100K-M / Detector: PIXEL / Date: Dec 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.42→43.7 Å / Num. obs: 444259 / % possible obs: 99.9 % / Redundancy: 5.66 % / CC1/2: 0.998 / Rsym value: 0.105 / Net I/σ(I): 4.74
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 5 % / Rmerge(I) obs: 0.84 / Num. unique obs: 32662 / CC1/2: 0.656 / Rpim(I) all: 0.183 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OJZ

4ojz


Resolution: 1.42→43.7 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.368 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1704 23668 5.1 %RANDOM
Rwork0.1611 ---
obs0.1616 444242 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 65.52 Å2 / Biso mean: 18.766 Å2 / Biso min: 8.46 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.42→43.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11637 0 43 1326 13006
Biso mean--18.69 25.88 -
Num. residues----1454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01912003
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211165
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9516256
X-RAY DIFFRACTIONr_angle_other_deg0.912325729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96251477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08724.984616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.223152045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6451548
X-RAY DIFFRACTIONr_chiral_restr0.0780.21719
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213874
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022883
LS refinement shellResolution: 1.424→1.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 1739 -
Rwork0.228 32954 -
all-34693 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1796-0.06880.05770.0694-0.03210.03070.00140.0058-0.0069-0.01080.00020.00830.0015-0.0179-0.00170.0078-0.0002-0.00450.03950.00060.01114.46855.972-19.083
20.26650.09190.10070.1233-0.0890.2065-0.02540.02680.0013-0.02680.0103-0.01180.01050.00620.01510.01910.00760.00940.03460.0080.005837.36159.964-28.86
30.0821-0.03470.0290.02210.00560.0686-0.00090.00120.00120.0004-0.0041-0.00280.00990.00610.0050.01620.0044-0.00010.01970.00980.019645.90652.581-3.525
40.8399-0.18370.19450.26460.11720.15990.03670.0467-0.07110.02060.0051-0.02040.03030.0273-0.04180.00720.0114-0.00520.0340.0040.033670.6739.904-1.349
50.3197-0.03520.01720.1033-0.03940.02780.00660.00370.00980.01660.0050.0140.01580.0056-0.01160.04220.0162-0.00510.00890.00270.012945.30536.72744.296
60.3713-0.17830.28461.7093-0.24140.227-0.0512-0.0659-0.02440.06760.0592-0.1818-0.0393-0.0521-0.0080.04920.00860.02170.026-0.01420.056639.60958.9955.031
70.0624-0.0488-0.00640.0574-0.02040.065-0.0108-0.0096-0.00050.00180.0007-0.0015-0.004-0.0110.01010.01620.0072-0.0090.0268-0.00170.014629.04463.78328.459
80.4083-0.14590.00690.4825-0.35710.2989-0.0353-0.04220.02040.03090.06710.0411-0.0288-0.0581-0.03180.03250.0367-0.01930.0442-0.01660.0237.20281.16526.745
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 225
2X-RAY DIFFRACTION2A226 - 260
3X-RAY DIFFRACTION3A261 - 688
4X-RAY DIFFRACTION4A689 - 751
5X-RAY DIFFRACTION5B25 - 225
6X-RAY DIFFRACTION6B226 - 260
7X-RAY DIFFRACTION7B261 - 688
8X-RAY DIFFRACTION8B689 - 751

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