[English] 日本語
Yorodumi
- PDB-7b8b: ADPG2 - ENDOPOLYGALACTURONASE FROM ARABIDOPSIS THALIANA -

+
Open data


ID or keywords:

Loading...

-
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 / pectin catabolic 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 / Pectin lyase fold / Pectin lyase fold/virulence factor
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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 / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 999 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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)

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more