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- PDB-7bm6: Structure-function analysis of a new PL17 oligoalginate lyase fro... -

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Basic information

Entry
Database: PDB / ID: 7bm6
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 / homologymannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / Heparinase II/III-like / Heparinase II/III-like protein / Alginate lyase domain / Alginate lyase / Chondroitin AC/alginate lyase / periplasmic space / Alginate lyase, family PL17
Function and homology information
Biological speciesZobellia galactanivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 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 19, 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)171,09311
Polymers170,1192
Non-polymers9749
Water16,430912
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-69 kcal/mol
Surface area49410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.132, 164.132, 168.370
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 / Sugars , 2 types, 4 molecules AB

#1: Protein Alginate lyase, family PL17


Mass: 85059.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The active site tyrosine Y274 was mutated to alanine Y247A The N-terminal peptide (1-23) was not included in recombinant construction defined by electron density
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
#2: Polysaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 352.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a1122A-1a_1-5][a11eEA-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-ManpA]{[(4+1)][a-L-4-deoxy-AllpA]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 919 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 912 / 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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: protein solution at 13.4 mg.ml-1, supplemented with 1.6 mM of oligo-mannuronate of DP3, was mixed with 0.2 micro-l of crystallization solution that contained 2.4 M sodium malonate (dibasic ...Details: protein solution at 13.4 mg.ml-1, supplemented with 1.6 mM of oligo-mannuronate of DP3, was mixed with 0.2 micro-l of crystallization solution that contained 2.4 M sodium malonate (dibasic monohydrate) and equilibrated against a reservoir containing 100 micro-l.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.16→45 Å / Num. obs: 137171 / % possible obs: 99.6 % / Redundancy: 21.16 % / CC1/2: 0.999 / Rpim(I) all: 0.054 / Rsym value: 0.12 / Net I/σ(I): 16.3
Reflection shellResolution: 2.16→2.21 Å / Redundancy: 18 % / Rmerge(I) obs: 1.57 / Num. unique obs: 7343 / CC1/2: 0.641 / Rpim(I) all: 0.356 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BJT

7bjt


Resolution: 2.16→45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.495 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 6752 4.9 %RANDOM
Rwork0.1532 ---
obs0.1547 130343 99.8 %-
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: 108.27 Å2 / Biso mean: 33.489 Å2 / Biso min: 17.67 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.16→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11619 0 60 912 12591
Biso mean--36.52 37.99 -
Num. residues----1454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01912030
X-RAY DIFFRACTIONr_bond_other_d0.0060.0211180
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.95216299
X-RAY DIFFRACTIONr_angle_other_deg1.013325770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28451482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80225.032616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.809152044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.841548
X-RAY DIFFRACTIONr_chiral_restr0.1070.21734
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213895
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022879
LS refinement shellResolution: 2.16→2.216 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 495 -
Rwork0.248 9390 -
all-9885 -
obs--97.76 %
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)
10.26890.0298-0.11840.1836-0.02960.18690.0021-0.00020.01690.0248-0.0063-0.0004-0.0168-0.03220.00410.00490.0027-0.00360.03080.00550.0362103.81391.28817.274
20.13330.05160.00390.09070.0770.16140.0089-0.0018-0.0322-0.0011-0.0056-0.0298-0.01050.041-0.00320.0013-0.0032-0.00210.03010.02240.058138.99787.4060.57
31.3828-0.6551-0.05730.9067-0.67060.8379-0.0728-0.0018-0.04430.0180.0251-0.00780.0253-0.00240.04770.0236-0.0094-0.01420.05330.01750.0304120.74577.9329.472
44.3081.29853.93890.43281.143.6592-0.06510.13830.0132-0.00710.04850.0085-0.07950.12520.01660.0222-0.01990.00540.028-0.00360.0574129.19495.911-23.726
50.21660.0688-0.09860.2154-0.07550.1733-0.01240.0099-0.0091-0.01710.00670.0165-0.04-0.00080.00580.0377-0.0167-0.00090.0129-0.00290.0319119.677101.13-42.138
60.33630.01860.36990.50760.13250.43860.0071-0.0497-0.03380.07540.00540.03580.0361-0.0621-0.01250.0334-0.01680.03450.0214-0.01620.0476108.53867.675-25.088
70.0579-0.25660.0133.5456-1.01110.4249-0.0230.0306-0.0005-0.0638-0.0247-0.17150.0129-0.030.04770.0857-0.03490.01860.042-0.03020.0583125.64779.991-53.89
82.11351.97342.28952.71633.46954.52290.0742-0.0771-0.03390.0484-0.088-0.00760.0493-0.12460.01380.0031-0.0025-0.00050.03630.00440.0482104.78880.235-0.922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 226
2X-RAY DIFFRACTION1A253 - 400
3X-RAY DIFFRACTION2A401 - 672
4X-RAY DIFFRACTION2A688 - 751
5X-RAY DIFFRACTION3A227 - 252
6X-RAY DIFFRACTION4A673 - 687
7X-RAY DIFFRACTION5B25 - 226
8X-RAY DIFFRACTION5B253 - 400
9X-RAY DIFFRACTION6B401 - 672
10X-RAY DIFFRACTION6B688 - 751
11X-RAY DIFFRACTION7B227 - 252
12X-RAY DIFFRACTION8B673 - 687

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