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- PDB-9k7l: Gamma-glutamyl peptidase 1 from Arabidopsis thaliana (H192N gamma... -

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Basic information

Entry
Database: PDB / ID: 9k7l
TitleGamma-glutamyl peptidase 1 from Arabidopsis thaliana (H192N gamma-Glu intermediate)
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 / GLUTAMIC ACID / Gamma-glutamyl peptidase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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)60,33110
Polymers59,5502
Non-polymers7818
Water8,071448
1
A: Gamma-glutamyl peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2576
Polymers29,7751
Non-polymers4825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area11630 Å2
MethodPISA
2
B: Gamma-glutamyl peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0734
Polymers29,7751
Non-polymers2983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.508, 75.109, 101.206
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: 29774.938 Da / Num. of mol.: 2 / Mutation: H192N
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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.28 Å3/Da / Density % sol: 46.1 %
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: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 20, 2023
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.59→46.15 Å / Num. obs: 71347 / % possible obs: 97 % / Redundancy: 6.6 % / Biso Wilson estimate: 13.89 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Net I/σ(I): 16.2
Reflection shellResolution: 1.59→1.62 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2936 / CC1/2: 0.791 / Rpim(I) all: 0.279 / % possible all: 82.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→46.15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.727 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20036 3570 5 %RANDOM
Rwork0.16644 ---
obs0.16816 67714 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.992 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0 Å2
2---0.63 Å2-0 Å2
3---0.73 Å2
Refinement stepCycle: 1 / Resolution: 1.59→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3990 0 50 448 4488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124160
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163937
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.8345600
X-RAY DIFFRACTIONr_angle_other_deg0.6141.7859109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.498519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23110749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024817
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02927
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_it1.8651.8412026
X-RAY DIFFRACTIONr_mcbond_other1.8661.842024
X-RAY DIFFRACTIONr_mcangle_it2.7553.292530
X-RAY DIFFRACTIONr_mcangle_other2.7553.292531
X-RAY DIFFRACTIONr_scbond_it3.6652.3432134
X-RAY DIFFRACTIONr_scbond_other3.6652.3442135
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6984.0513071
X-RAY DIFFRACTIONr_long_range_B_refined6.926.325052
X-RAY DIFFRACTIONr_long_range_B_other6.90126.325053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.592→1.633 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 230 -
Rwork0.249 4264 -
obs--83.69 %

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