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- PDB-7b8b: ADPG2 - ENDOPOLYGALACTURONASE FROM ARABIDOPSIS THALIANA -

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Basic information

Entry
Database: PDB / ID: 7b8b
TitleADPG2 - ENDOPOLYGALACTURONASE FROM ARABIDOPSIS THALIANA
ComponentsPolygalacturonase ADPG2
KeywordsHYDROLASE / Pectinase / Beta-sheets / GH28
Function / homology
Function and homology information


cell wall modification involved in abscission / fruit dehiscence / endo-polygalacturonase / floral organ abscission / anther dehiscence / polygalacturonase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Polygalacturonase active site. / 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
PHOSPHATE ION / Polygalacturonase ADPG2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id
Revision 1.3Nov 13, 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 ADPG2
B: Polygalacturonase ADPG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4663
Polymers90,3712
Non-polymers951
Water17,997999
1
A: Polygalacturonase ADPG2


Theoretical massNumber of molelcules
Total (without water)45,1851
Polymers45,1851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polygalacturonase ADPG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2802
Polymers45,1851
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.780, 88.560, 113.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 40 through 90 or resid 92...
d_2ens_1(chain "B" and (resid 40 through 90 or resid 92...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11THRTHRLYSLYSAA40 - 9040 - 90
d_12ILEILELEULEUAA92 - 9492 - 94
d_13GLYGLYLYSLYSAA96 - 17796 - 177
d_14LEULEULEULEUAA179179
d_15ILEILESERSERAA180 - 205180 - 205
d_16VALVALTHRTHRAA207 - 224207 - 224
d_17THRTHRGLYGLYAA226 - 237226 - 237
d_18GLYGLYGLYGLYAA239239
d_19ASPASPILEILEAA240 - 243240 - 243
d_110ILEILEILEILEAA245245
d_111SERSERGLNGLNAA247 - 253247 - 253
d_112ASNASNASNASNAA255255
d_113ASPASPILEILEAA256 - 257256 - 257
d_114GLYGLYGLYGLYAA260260
d_115PROPROGLYGLYAA261 - 306261 - 306
d_116ALAALAALAALAAA308308
d_117ASNASNALAALAAA310 - 359310 - 359
d_118GLUGLUGLUGLUAA361361
d_119ASNASNALAALAAA362 - 401362 - 401
d_120LEULEULEULEUAA403403
d_121PROPROCYSCYSAA404 - 406404 - 406
d_21THRTHRLYSLYSBB40 - 9040 - 90
d_22ILEILEILEILEBB9292
d_23GLNGLNLEULEUBB93 - 9493 - 94
d_24GLYGLYGLYGLYBB9696
d_25PROPROLYSLYSBB97 - 17797 - 177
d_26LEULEUSERSERBB179 - 205179 - 205
d_27VALVALVALVALBB207207
d_28VALVALTHRTHRBB208 - 224208 - 224
d_29THRTHRTHRTHRBB226226
d_210GLNGLNGLYGLYBB227 - 237227 - 237
d_211GLYGLYILEILEBB239 - 243239 - 243
d_212ILEILEILEILEBB245245
d_213SERSERGLNGLNBB247 - 253247 - 253
d_214ASNASNILEILEBB255 - 257255 - 257
d_215GLYGLYGLYGLYBB260 - 306260 - 306
d_216ALAALAALAALABB308308
d_217ASNASNASNASNBB310310
d_218ILEILEALAALABB311 - 359311 - 359
d_219GLUGLUALAALABB361 - 401361 - 401
d_220LEULEUCYSCYSBB403 - 406403 - 406

NCS oper: (Code: givenMatrix: (0.398695745494, -0.780964916558, 0.480765537065), (-0.737797723669, -0.584511223688, -0.337640560851), (0.544698284808, -0.220091863748, -0.80923627578)Vector: 4. ...NCS oper: (Code: given
Matrix: (0.398695745494, -0.780964916558, 0.480765537065), (-0.737797723669, -0.584511223688, -0.337640560851), (0.544698284808, -0.220091863748, -0.80923627578)
Vector: 4.02874859792, 24.1953872733, 16.9363313432)

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Components

#1: Protein Polygalacturonase ADPG2 / PG ADPG2 / Pectinase ADPG2 / Protein ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 2


Mass: 45185.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADPG2, PGAZAT, At2g41850, T11A7.5 / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q8RY29, endo-polygalacturonase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium malonate dibasic monohydrate, 20 % w/v PEG 3350 (E12 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 EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.03→47.9 Å / Num. obs: 47350 / % possible obs: 99.92 % / Redundancy: 2 % / Biso Wilson estimate: 20.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.021 / Rrim(I) all: 0.029 / Net I/σ(I): 16.9
Reflection shellResolution: 2.03→2.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.323 / Num. unique obs: 4654 / CC1/2: 0.893 / Rrim(I) all: 0.456 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
pointlessdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7B7A

7b7a


Resolution: 2.03→47.89 Å / SU ML: 0.2413 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.3408
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2297 2368 5 %
Rwork0.188 44975 -
obs0.1901 47343 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.1 Å2
Refinement stepCycle: LAST / Resolution: 2.03→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5459 0 5 1057 6521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00565653
X-RAY DIFFRACTIONf_angle_d0.89927693
X-RAY DIFFRACTIONf_chiral_restr0.0601909
X-RAY DIFFRACTIONf_plane_restr0.00541014
X-RAY DIFFRACTIONf_dihedral_angle_d14.92742065
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.34494034999 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.070.331350.29032566X-RAY DIFFRACTION98.87
2.07-2.120.28611380.26282624X-RAY DIFFRACTION99.96
2.12-2.170.27471370.24942592X-RAY DIFFRACTION99.96
2.17-2.220.25381370.2322611X-RAY DIFFRACTION100
2.22-2.280.28011390.21932633X-RAY DIFFRACTION99.96
2.28-2.350.26811360.2112586X-RAY DIFFRACTION100
2.35-2.430.30241390.21122638X-RAY DIFFRACTION100
2.43-2.510.27641380.19752624X-RAY DIFFRACTION99.96
2.51-2.610.23461380.19162626X-RAY DIFFRACTION100
2.61-2.730.23171390.18632642X-RAY DIFFRACTION100
2.73-2.880.231390.19372638X-RAY DIFFRACTION100
2.88-3.060.25031390.19022641X-RAY DIFFRACTION100
3.06-3.290.19871400.17492654X-RAY DIFFRACTION100
3.29-3.620.19741400.15662663X-RAY DIFFRACTION100
3.62-4.150.18021410.14422676X-RAY DIFFRACTION100
4.15-5.220.16471430.13192724X-RAY DIFFRACTION99.86
5.23-47.890.25361500.21122837X-RAY DIFFRACTION99.97

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