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- PDB-8ikw: A complex structure of PGIP-PG -

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Basic information

Entry
Database: PDB / ID: 8ikw
TitleA complex structure of PGIP-PG
Components
  • Endo-polygalacturonase
  • Polygalacturonase inhibitor 2
KeywordsHYDROLASE / PGIP / polygalacturonase
Function / homology
Function and homology information


endo-polygalacturonase / polygalacturonase activity / pectin catabolic process / defense response / cell wall organization / extracellular region / membrane
Similarity search - Function
: / : / Polygalacturonase active site. / Glycoside hydrolase, family 28 / Glycosyl hydrolases family 28 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Parallel beta-helix repeat / Parallel beta-helix repeats / Leucine Rich Repeat ...: / : / Polygalacturonase active site. / Glycoside hydrolase, family 28 / Glycosyl hydrolases family 28 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Parallel beta-helix repeat / Parallel beta-helix repeats / Leucine Rich Repeat / Pectin lyase fold / Pectin lyase fold/virulence factor / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
endo-polygalacturonase / Polygalacturonase inhibitor 2
Similarity search - Component
Biological speciesPhaseolus vulgaris (common bean)
Fusarium phyllophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 16, 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

Downloads & links

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Assembly

Deposited unit
A: Polygalacturonase inhibitor 2
B: Endo-polygalacturonase
C: Polygalacturonase inhibitor 2
E: Polygalacturonase inhibitor 2
G: Polygalacturonase inhibitor 2
D: Endo-polygalacturonase
F: Endo-polygalacturonase
H: Endo-polygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,16520
Polymers280,9858
Non-polymers6,18012
Water43,1462395
1
A: Polygalacturonase inhibitor 2
B: Endo-polygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9745
Polymers70,2462
Non-polymers1,7283
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Polygalacturonase inhibitor 2
D: Endo-polygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5205
Polymers70,2462
Non-polymers1,2733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Polygalacturonase inhibitor 2
F: Endo-polygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1525
Polymers70,2462
Non-polymers1,9063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Polygalacturonase inhibitor 2
H: Endo-polygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5205
Polymers70,2462
Non-polymers1,2733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.727, 105.218, 113.821
Angle α, β, γ (deg.)63.93, 89.12, 86.27
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Polygalacturonase inhibitor 2 / Polygalacturonase-inhibiting protein 2 / PGIP-2


Mass: 34023.824 Da / Num. of mol.: 4 / Mutation: N303D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaseolus vulgaris (common bean) / Gene: PGIP2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P58822
#2: Protein
Endo-polygalacturonase


Mass: 36222.492 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium phyllophilum (fungus) / Gene: FPHYL_6983 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A8H5NAM9

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Sugars , 5 types, 12 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 716.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4][LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1-2/a3-b1_a4-c1_a6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 1 types, 2395 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2395 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1% w/v n-Octyl-beta-D-glucoside, 0.1M Na citrate tribasic dihydrate pH 5.5, 22% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 202233 / % possible obs: 85.6 % / Redundancy: 1.2 % / CC1/2: 0.975 / Rmerge(I) obs: 0.157 / Χ2: 0.141 / Net I/σ(I): 6 / Num. measured all: 447435
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.93-1.961.20.603179550.81185.8
1.96-21.20.526179390.787185.1
2-2.041.20.463176750.779184.7
2.04-2.081.20.416173170.841182.2
2.08-2.121.20.364174120.92182.3
2.12-2.171.20.326181750.868186.6
2.17-2.231.20.287176900.984184.7
2.23-2.291.20.242175001.024183.4
2.29-2.361.30.224185611.028188.4
2.36-2.431.30.218185971.055188.3
2.43-2.521.30.192185131.162187.7
2.52-2.621.20.169180901.311186.1
2.62-2.741.20.151178441.442185.2
2.74-2.881.30.134182921.464187.5
2.88-3.061.20.12180641.582185.9
3.06-3.31.30.099187511.85189.4
3.3-3.631.30.086182362.314186.7
3.63-4.161.20.081176473.16184
4.16-5.241.20.084180113.989185.6
5.24-501.20.095172994.066182.6

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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: 1.94→34.29 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 10099 5 %
Rwork0.1919 --
obs0.1939 201788 95.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→34.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19648 0 410 2395 22453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01520434
X-RAY DIFFRACTIONf_angle_d1.91527846
X-RAY DIFFRACTIONf_dihedral_angle_d10.3392955
X-RAY DIFFRACTIONf_chiral_restr0.1153351
X-RAY DIFFRACTIONf_plane_restr0.0193604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.960.30822670.24434913X-RAY DIFFRACTION73
1.96-1.990.2823220.2336323X-RAY DIFFRACTION95
1.99-2.010.26623260.22526457X-RAY DIFFRACTION96
2.01-2.030.30053340.23096417X-RAY DIFFRACTION95
2.03-2.060.27353540.22646313X-RAY DIFFRACTION95
2.06-2.090.26673250.22156415X-RAY DIFFRACTION95
2.09-2.120.28923360.21846424X-RAY DIFFRACTION96
2.12-2.150.28113630.21646478X-RAY DIFFRACTION96
2.15-2.180.28353370.20846353X-RAY DIFFRACTION96
2.18-2.220.28623200.216441X-RAY DIFFRACTION96
2.22-2.260.25493240.20856441X-RAY DIFFRACTION96
2.26-2.30.2323120.20226549X-RAY DIFFRACTION96
2.3-2.340.25713270.19896417X-RAY DIFFRACTION96
2.34-2.390.23873410.20546503X-RAY DIFFRACTION97
2.39-2.440.26523290.20346531X-RAY DIFFRACTION97
2.44-2.50.2463430.20056447X-RAY DIFFRACTION97
2.5-2.560.25923420.20366427X-RAY DIFFRACTION96
2.56-2.630.23683360.1896536X-RAY DIFFRACTION97
2.63-2.710.25333340.20316523X-RAY DIFFRACTION97
2.71-2.80.26033660.20296431X-RAY DIFFRACTION97
2.8-2.90.26073520.20416467X-RAY DIFFRACTION97
2.9-3.010.24443740.20146516X-RAY DIFFRACTION97
3.01-3.150.24053580.20056536X-RAY DIFFRACTION97
3.15-3.320.20943270.19276493X-RAY DIFFRACTION97
3.32-3.520.21763720.18196446X-RAY DIFFRACTION97
3.52-3.80.20293200.16586454X-RAY DIFFRACTION96
3.8-4.180.17093370.15636419X-RAY DIFFRACTION96
4.18-4.780.17543680.14476346X-RAY DIFFRACTION95
4.78-6.020.19873510.17666463X-RAY DIFFRACTION97
6.02-34.290.21043020.19086210X-RAY DIFFRACTION92

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