[English] 日本語
Yorodumi
- PDB-9k7j: Gamma-glutamyl peptidase 1 from Arabidopsis thaliana (ligand-free) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9k7j
TitleGamma-glutamyl peptidase 1 from Arabidopsis thaliana (ligand-free)
ComponentsGamma-glutamyl peptidase 1
KeywordsHYDROLASE / Peptidase
Function / homology
Function and homology information


glucosinolate gamma-glutamyl hydrolase / glucosinolate metabolic process / camalexin biosynthetic process / gamma-glutamyl-peptidase activity / secretory vesicle / peptidase activity / proteolysis / plasma membrane / cytosol
Similarity search - Function
Glutamine amidotransferase domain containing protein ChyE-like / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
ACETATE ION / Gamma-glutamyl peptidase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSone, K. / Kashima, T. / Miyanaga, A. / Fushinobu, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To Be Published
Title: Crystal structures of Gamma-glutamyl peptidase 1 from Arabidopsis thaliana
Authors: Sone, K. / Ito, T. / Arakawa, T. / Kashima, T. / Miyanaga, A. / Ohkama-Ohtsu, N. / Fushinobu, S.
#1: Journal: Plant J. / Year: 2022
Title: Glutathione degradation activity of Gamma-glutamyl peptidase 1 manifests its dual roles in primary and secondary sulfur metabolism in Arabidopsis.
Authors: Ito, T. / Kitaiwa, T. / Nishizono, K. / Umahashi, M. / Miyaji, S. / Agake, S.I. / Kuwahara, K. / Yokoyama, T. / Fushinobu, S. / Maruyama-Nakashita, A. / Sugiyama, R. / Sato, M. / Inaba, J. / ...Authors: Ito, T. / Kitaiwa, T. / Nishizono, K. / Umahashi, M. / Miyaji, S. / Agake, S.I. / Kuwahara, K. / Yokoyama, T. / Fushinobu, S. / Maruyama-Nakashita, A. / Sugiyama, R. / Sato, M. / Inaba, J. / Hirai, M.Y. / Ohkama-Ohtsu, N.
History
DepositionOct 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamma-glutamyl peptidase 1
B: Gamma-glutamyl peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8085
Polymers59,5982
Non-polymers2103
Water6,251347
1
A: Gamma-glutamyl peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8582
Polymers29,7991
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11330 Å2
MethodPISA
2
B: Gamma-glutamyl peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9503
Polymers29,7991
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.542, 75.589, 103.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Gamma-glutamyl peptidase 1


Mass: 29798.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GGP1, At4g30530 / Plasmid: pDEST-17 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9M0A7, glucosinolate gamma-glutamyl hydrolase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: sodium acetate, sodium dihydrogen phsophate, di-potassium hydrogen phsophate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2023
RadiationMonochromator: A liquid nitrogen cooled Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.72 Å / Num. obs: 45322 / % possible obs: 100 % / Redundancy: 1.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.057 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2888 / CC1/2: 0.663 / Rpim(I) all: 0.467 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.72 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.376 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2188 2358 5.2 %RANDOM
Rwork0.16985 ---
obs0.17238 42964 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.361 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å2-0 Å2
2--0.04 Å2-0 Å2
3---1.14 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 14 347 4298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124122
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163893
X-RAY DIFFRACTIONr_angle_refined_deg2.4411.8345562
X-RAY DIFFRACTIONr_angle_other_deg0.7921.7849007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6925505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.795518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31610739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1170.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02920
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0762.0532013
X-RAY DIFFRACTIONr_mcbond_other3.0672.0532010
X-RAY DIFFRACTIONr_mcangle_it4.4173.6662519
X-RAY DIFFRACTIONr_mcangle_other4.4163.6662520
X-RAY DIFFRACTIONr_scbond_it4.8862.6172109
X-RAY DIFFRACTIONr_scbond_other4.8852.6172110
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3044.5123044
X-RAY DIFFRACTIONr_long_range_B_refined8.48224.814706
X-RAY DIFFRACTIONr_long_range_B_other8.48224.814706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 197 -
Rwork0.302 3100 -
obs--99.88 %

+
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