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- PDB-8ikx: An Arabidopsis polygalacturonase PGLR -

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Basic information

Entry
Database: PDB / ID: 8ikx
TitleAn Arabidopsis polygalacturonase PGLR
ComponentsPectin lyase-like superfamily protein
KeywordsHYDROLASE / polygalacturonase
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 / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Pectin lyase-like superfamily protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsXiao, Y. / Chai, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Science / Year: 2024
Title: A plant mechanism of hijacking pathogen virulence factors to trigger innate immunity.
Authors: Xiao, Y. / Sun, G. / Yu, Q. / Gao, T. / Zhu, Q. / Wang, R. / Huang, S. / Han, Z. / Cervone, F. / Yin, H. / Qi, T. / Wang, Y. / Chai, J.
History
DepositionMar 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 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)42,9893
Polymers41,5331
Non-polymers1,4562
Water8,989499
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.212, 43.540, 63.478
Angle α, β, γ (deg.)94.590, 99.990, 110.550
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: 41532.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g14650, AT5G14650, T15N1.140, T15N1_140 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9LYJ5
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M trimethylamine N-oxide dihydrate, 0.1M Tris pH 8.5, 20% w/v PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 58730 / % possible obs: 92.9 % / Redundancy: 1.7 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.088 / Χ2: 0.064 / Net I/σ(I): 8.9 / Num. measured all: 193031
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.5-1.531.40.23349211.106180.9
1.53-1.551.50.21853051.08185.8
1.55-1.581.50.22254451.193188.6
1.58-1.621.60.21755041.121190.4
1.62-1.651.60.23354921.185190.4
1.65-1.691.60.24756051.139191
1.69-1.731.60.22356651.21191.7
1.73-1.781.70.20556861.212192.6
1.78-1.831.70.17956801.195193.9
1.83-1.891.70.14859091.28194.4
1.89-1.961.70.13357611.4194.2
1.96-2.041.70.11956861.395193.9
2.04-2.131.70.10858471.42194.8
2.13-2.241.80.09657941.433195.2
2.24-2.381.80.08559161.467196.3
2.38-2.561.80.07459151.432196.3
2.56-2.821.80.06459411.495197
2.82-3.231.90.0559421.387197.1
3.23-4.071.70.03859501.346197.1
4.07-501.80.03359371.207196.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXv1.20.1-4487refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→31.61 Å / SU ML: 0.1335 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.0592
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1792 2965 5.06 %
Rwork0.158 55612 -
obs0.1591 58577 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 97 499 3501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083060
X-RAY DIFFRACTIONf_angle_d1.05154153
X-RAY DIFFRACTIONf_chiral_restr0.1019500
X-RAY DIFFRACTIONf_plane_restr0.0083523
X-RAY DIFFRACTIONf_dihedral_angle_d6.683471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.23881390.20392340X-RAY DIFFRACTION84.64
1.52-1.550.20431410.18682525X-RAY DIFFRACTION90.68
1.55-1.580.23621360.18222544X-RAY DIFFRACTION92.29
1.58-1.610.23181320.17862580X-RAY DIFFRACTION93.16
1.61-1.640.21061270.18232647X-RAY DIFFRACTION94
1.64-1.680.21111250.17852617X-RAY DIFFRACTION94.29
1.68-1.720.21821470.1812629X-RAY DIFFRACTION94.91
1.72-1.760.20811570.17492627X-RAY DIFFRACTION94.95
1.76-1.810.22081290.18152666X-RAY DIFFRACTION95.65
1.81-1.860.22051420.17052652X-RAY DIFFRACTION96.31
1.86-1.920.17871360.15822650X-RAY DIFFRACTION96.1
1.92-1.990.18021440.14922690X-RAY DIFFRACTION96.59
1.99-2.070.18361410.15282721X-RAY DIFFRACTION96.72
2.07-2.160.15991530.15632671X-RAY DIFFRACTION97.18
2.16-2.280.14971250.14952722X-RAY DIFFRACTION97.33
2.28-2.420.2051420.15142704X-RAY DIFFRACTION97.6
2.42-2.610.19011410.15842720X-RAY DIFFRACTION97.91
2.61-2.870.17821300.15272724X-RAY DIFFRACTION98.18
2.87-3.280.16741380.15352743X-RAY DIFFRACTION98.56
3.28-4.130.16361750.1372713X-RAY DIFFRACTION98.97
4.13-31.610.14921650.16092727X-RAY DIFFRACTION98.94

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