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- PDB-7b7a: ENDO-POLYGALACTURONASE FROM ARABIDOPSIS THALIANA -

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Basic information

Entry
Database: PDB / ID: 7b7a
TitleENDO-POLYGALACTURONASE FROM ARABIDOPSIS THALIANA
ComponentsPectin lyase-like superfamily protein
KeywordsHYDROLASE / Pectinase / Beta-sheets
Function / homology
Function and homology information


plant-type cell wall modification / polygalacturonase activity / plant-type cell wall / carbohydrate metabolic process / lyase activity / extracellular region
Similarity search - Function
Glycoside hydrolase, family 28 / Glycosyl hydrolases family 28 / 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 / Mainly Beta
Similarity search - Domain/homology
Pectin lyase-like superfamily protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSafran, J. / Tabi, W. / Habrylo, O. / Bouckaert, J. / Lefebvre, V. / Senechal, F. / Pelloux, J.
Funding supportEuropean Union, France, 2items
OrganizationGrant numberCountry
European Regional Development FundEuropean Union
Agence Nationale de la Recherche (ANR)CARAPEC-Region Hauts de France France
CitationJournal: Plant Cell / Year: 2023
Title: Plant polygalacturonase structures specify enzyme dynamics and processivities to fine-tune cell wall pectins.
Authors: Safran, J. / Tabi, W. / Ung, V. / Lemaire, A. / Habrylo, O. / Bouckaert, J. / Rouffle, M. / Voxeur, A. / Pongrac, P. / Bassard, S. / Molinie, R. / Fontaine, J.X. / Pilard, S. / Pau-Roblot, C. ...Authors: Safran, J. / Tabi, W. / Ung, V. / Lemaire, A. / Habrylo, O. / Bouckaert, J. / Rouffle, M. / Voxeur, A. / Pongrac, P. / Bassard, S. / Molinie, R. / Fontaine, J.X. / Pilard, S. / Pau-Roblot, C. / Bonnin, E. / Larsen, D.S. / Morel-Rouhier, M. / Girardet, J.M. / Lefebvre, V. / Senechal, F. / Mercadante, D. / Pelloux, J.
History
DepositionDec 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pectin lyase-like superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5373
Polymers46,0401
Non-polymers1,4972
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint28 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.970, 41.830, 63.330
Angle α, β, γ (deg.)93.250, 99.860, 114.950
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Pectin lyase-like superfamily protein / Polygalacturonase-like protein


Mass: 46039.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g14650, T15N1.140, T15N1_140 / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q9LYJ5
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium fluoride, 0.1 M Bis-Tris propane pH 8.5, 20 % w/v PEG 3350 (H1 condition, PACT premier plate)

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.3→34.5 Å / Num. obs: 83670 / % possible obs: 96.16 % / Redundancy: 9.1 % / Biso Wilson estimate: 14.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.026 / Net I/σ(I): 16.2
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.777 / Num. unique obs: 8043 / CC1/2: 0.864 / Rpim(I) all: 0.32 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHASERphasing
XSCALEdata scaling
Aimlessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RMG

1rmg


Resolution: 1.3→34.5 Å / SU ML: 0.1169 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 17.6227
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1774 4182 5 %
Rwork0.1419 79452 -
obs0.1437 83634 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.31 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 100 607 3616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01233266
X-RAY DIFFRACTIONf_angle_d1.53094473
X-RAY DIFFRACTIONf_chiral_restr0.1109532
X-RAY DIFFRACTIONf_plane_restr0.0113582
X-RAY DIFFRACTIONf_dihedral_angle_d15.76141216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.25221340.2022535X-RAY DIFFRACTION91.69
1.31-1.330.25911320.20222511X-RAY DIFFRACTION92.32
1.33-1.350.25691350.19222582X-RAY DIFFRACTION92.07
1.35-1.360.2111330.18132528X-RAY DIFFRACTION92.36
1.36-1.380.21231330.16872534X-RAY DIFFRACTION92.67
1.38-1.40.23421380.16782615X-RAY DIFFRACTION93.07
1.4-1.420.21291330.16952521X-RAY DIFFRACTION93.06
1.42-1.440.2111360.16272593X-RAY DIFFRACTION93.17
1.44-1.460.22051340.17112549X-RAY DIFFRACTION94.97
1.46-1.490.19891420.15512684X-RAY DIFFRACTION95.76
1.49-1.510.20681390.13932652X-RAY DIFFRACTION95.91
1.51-1.540.17511390.12912637X-RAY DIFFRACTION96.06
1.54-1.570.14481400.12462645X-RAY DIFFRACTION95.97
1.57-1.60.17951390.13022644X-RAY DIFFRACTION95.7
1.6-1.640.16811390.13242636X-RAY DIFFRACTION96.35
1.64-1.680.17961410.13122689X-RAY DIFFRACTION96.79
1.68-1.720.17681390.12852642X-RAY DIFFRACTION96.83
1.72-1.760.18141430.13252701X-RAY DIFFRACTION97.2
1.76-1.820.17231410.13152692X-RAY DIFFRACTION97.66
1.82-1.870.15921400.12482646X-RAY DIFFRACTION97.51
1.87-1.940.15831430.12032719X-RAY DIFFRACTION97.78
1.94-2.020.16061410.12222680X-RAY DIFFRACTION98.22
2.02-2.110.16411430.12532729X-RAY DIFFRACTION98.36
2.11-2.220.15691440.12392730X-RAY DIFFRACTION98.56
2.22-2.360.15581430.12612713X-RAY DIFFRACTION98.69
2.36-2.540.16221440.13812733X-RAY DIFFRACTION98.87
2.54-2.80.17271430.14462724X-RAY DIFFRACTION99.2
2.8-3.210.15721440.14192739X-RAY DIFFRACTION99.07
3.21-4.040.16751430.13292718X-RAY DIFFRACTION99.44
4.04-34.50.21061440.17432731X-RAY DIFFRACTION98.8

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