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- PDB-1ogq: The crystal structure of PGIP (polygalacturonase inhibiting prote... -

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Basic information

Entry
Database: PDB / ID: 1ogq
TitleThe crystal structure of PGIP (polygalacturonase inhibiting protein), a leucine rich repeat protein involved in plant defense
ComponentsPOLYGALACTURONASE INHIBITING PROTEIN
KeywordsINHIBITOR / POLYGALACTURONASE INHIBITING PROTEIN
Function / homology
Function and homology information


defense response / extracellular region / membrane
Similarity search - Function
: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Polygalacturonase inhibitor 2
Similarity search - Component
Biological speciesPHASEOLUS VULGARIS (French bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.7 Å
AuthorsDi Matteo, A. / Federici, L. / Mattei, B. / Salvi, G. / Johnson, K.A. / Savino, C. / De Lorenzo, G. / Tsernoglou, D. / Cervone, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: The Crystal Structure of Polygalacturonase-Inhibiting Protein (Pgip), a Leucine-Rich Repeat Protein Involved in Plant Defense
Authors: Di Matteo, A. / Federici, L. / Mattei, B. / Salvi, G. / Johnson, K.A. / Savino, C. / De Lorenzo, G. / Tsernoglou, D. / Cervone, F.
History
DepositionMay 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYGALACTURONASE INHIBITING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9676
Polymers34,0231
Non-polymers9445
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)134.840, 65.450, 34.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein POLYGALACTURONASE INHIBITING PROTEIN / PGIP-2


Mass: 34022.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHASEOLUS VULGARIS (French bean) / Production host: NICOTIANA BENTHAMIANA (plant) / References: UniProt: P58822
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINHIBITOR OF FUNGAL POLYGALACTURONASE. THE PROTEIN IS AN IMPORTANT FACTOR FOR PLANT RESISTANCE TO ...INHIBITOR OF FUNGAL POLYGALACTURONASE. THE PROTEIN IS AN IMPORTANT FACTOR FOR PLANT RESISTANCE TO PHYTOPATHOGENIC FUNGI.
Sequence detailsTHE PGIP2_PHAVU IN THE SWISS-PROT DATABASE CONTAINS THE SIGNAL PEPTIDE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-30 %(w/v)PEG40001reservoir
20.18-0.2 Mammonium acetate1reservoir
30.1 Msodium acetate1reservoirpH4.6
44.0 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 34715 / % possible obs: 94.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.4
Reflection shellHighest resolution: 1.7 Å / Rmerge(I) obs: 0.45 / % possible all: 65.5
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Num. measured all: 330460 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 65.5 % / Rmerge(I) obs: 0.45

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.7→25 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.24 -5 %RANDOM
Rwork0.19 ---
obs-34715 94.1 %-
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2392 0 60 320 2772
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.015
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg2.6

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