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- PDB-9k7k: Gamma-glutamyl peptidase 1 from Arabidopsis thaliana (inactive form) -

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Basic information

Entry
Database: PDB / ID: 9k7k
TitleGamma-glutamyl peptidase 1 from Arabidopsis thaliana (inactive form)
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: 2.04 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. / Yamada, C. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,8676
Polymers59,5982
Non-polymers2694
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.354, 75.329, 102.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 3 / 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.: 126 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: sodium acetate, sodium dihydrogen phsophate, di-potassium hydrogen phsophate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→46.55 Å / Num. obs: 36242 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.04 / Net I/σ(I): 13.5
Reflection shellResolution: 2.04→2.1 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2787 / CC1/2: 0.895 / Rpim(I) all: 0.232 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→46.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.194 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23323 1878 5.2 %RANDOM
Rwork0.17655 ---
obs0.17955 34305 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: 30.604 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.94 Å20 Å2
3---0.88 Å2
Refinement stepCycle: 1 / Resolution: 2.04→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3930 0 18 126 4074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124127
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163899
X-RAY DIFFRACTIONr_angle_refined_deg2.5541.8355562
X-RAY DIFFRACTIONr_angle_other_deg0.8151.7879021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6565505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.867518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43210748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1180.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02924
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_it3.9612.7112014
X-RAY DIFFRACTIONr_mcbond_other3.8962.7092011
X-RAY DIFFRACTIONr_mcangle_it5.1144.8332519
X-RAY DIFFRACTIONr_mcangle_other5.1134.8362520
X-RAY DIFFRACTIONr_scbond_it5.6013.2982113
X-RAY DIFFRACTIONr_scbond_other5.63.2982114
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0295.7643044
X-RAY DIFFRACTIONr_long_range_B_refined9.06432.54609
X-RAY DIFFRACTIONr_long_range_B_other9.06532.54609
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.044→2.097 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 122 -
Rwork0.201 2544 -
obs--100 %

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