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- PDB-6gmo: Plant glutamate cysteine ligase (GCL) in complex with non-reducin... -

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Basic information

Entry
Database: PDB / ID: 6gmo
TitlePlant glutamate cysteine ligase (GCL) in complex with non-reducing GSH (GSM)
ComponentsGlutamate--cysteine ligase, chloroplastic
KeywordsLIGASE / Glutathione synthesis / Complex
Function / homology
Function and homology information


oxoacid metabolic process / cellular modified amino acid biosynthetic process / glutamate-cysteine ligase / glutamate-cysteine ligase activity / glutathione biosynthetic process / chloroplast / ATP binding
Similarity search - Function
Glutamate--cysteine ligase, plant-type / Glutamate--cysteine ligase, bacteria and plant / Glutamate--cysteine ligase, GCS2 / Glutamate-cysteine ligase family 2(GCS2) / Creatine Kinase; Chain A, domain 2 - #20 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / L-GAMMA-GLUTAMYL-S-METHYLCYSTEINYLGLYCINE / Glutamate--cysteine ligase, chloroplastic
Similarity search - Component
Biological speciesBrassica juncea (brown mustard)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLenherr, E.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP1710 Germany
CitationJournal: Biochem.J. / Year: 2019
Title: Plant glutathione biosynthesis revisited: redox-mediated activation of glutamylcysteine ligase does not require homo-dimerization.
Authors: Yang, Y. / Lenherr, E.D. / Gromes, R. / Wang, S. / Wirtz, M. / Hell, R. / Peskan-Berghofer, T. / Scheffzek, K. / Rausch, T.
History
DepositionMay 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate--cysteine ligase, chloroplastic
B: Glutamate--cysteine ligase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,41110
Polymers101,4182
Non-polymers9948
Water22,3391240
1
A: Glutamate--cysteine ligase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2065
Polymers50,7091
Non-polymers4974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate--cysteine ligase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2065
Polymers50,7091
Non-polymers4974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.770, 109.860, 84.750
Angle α, β, γ (deg.)90.00, 98.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamate--cysteine ligase, chloroplastic / Gamma-ECS / GCS / Gamma-glutamylcysteine synthetase


Mass: 50708.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica juncea (brown mustard) / Gene: GSH1, ECS1 / Production host: Escherichia coli (E. coli) / References: UniProt: O23736, glutamate-cysteine ligase

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Non-polymers , 5 types, 1248 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GSM / L-GAMMA-GLUTAMYL-S-METHYLCYSTEINYLGLYCINE / S-METHYL-GLUTATHIONE


Mass: 321.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1240 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaAc, 20 % (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.975 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.75→19.89 Å / Num. obs: 105763 / % possible obs: 98.9 % / Redundancy: 3.72 % / Rsym value: 0.082 / Net I/σ(I): 14.09
Reflection shellResolution: 1.75→1.8 Å

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gwd

2gwd


Resolution: 1.75→19.716 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.92
RfactorNum. reflection% reflection
Rfree0.1975 5289 5 %
Rwork0.1634 --
obs0.1651 105758 98.96 %
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Bsol: 58.102 Å2 / ksol: 0.367 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3278 Å20 Å2-0.1528 Å2
2--0.0733 Å2-0 Å2
3----0.4011 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7019 0 64 1245 8328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017398
X-RAY DIFFRACTIONf_angle_d1.39710028
X-RAY DIFFRACTIONf_dihedral_angle_d14.3222817
X-RAY DIFFRACTIONf_chiral_restr0.1031065
X-RAY DIFFRACTIONf_plane_restr0.011310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.33261570.27842971X-RAY DIFFRACTION88
1.7699-1.79070.30951630.26173110X-RAY DIFFRACTION93
1.7907-1.81250.26711720.25073258X-RAY DIFFRACTION97
1.8125-1.83540.29891790.24533411X-RAY DIFFRACTION99
1.8354-1.85960.27161750.23213318X-RAY DIFFRACTION99
1.8596-1.8850.28411760.22183351X-RAY DIFFRACTION99
1.885-1.91190.27331770.21363344X-RAY DIFFRACTION99
1.9119-1.94040.25321770.19593365X-RAY DIFFRACTION100
1.9404-1.97070.22521770.18383366X-RAY DIFFRACTION99
1.9707-2.0030.19861750.17683326X-RAY DIFFRACTION100
2.003-2.03750.21721790.17363411X-RAY DIFFRACTION100
2.0375-2.07450.24471770.17613350X-RAY DIFFRACTION100
2.0745-2.11440.21861770.16633361X-RAY DIFFRACTION100
2.1144-2.15750.21041760.16423358X-RAY DIFFRACTION100
2.1575-2.20430.22121770.15833366X-RAY DIFFRACTION100
2.2043-2.25560.20581790.15163383X-RAY DIFFRACTION100
2.2556-2.31190.17981760.14953355X-RAY DIFFRACTION100
2.3119-2.37430.18551760.14933345X-RAY DIFFRACTION100
2.3743-2.4440.19951810.15293432X-RAY DIFFRACTION100
2.444-2.52280.20891750.15043324X-RAY DIFFRACTION100
2.5228-2.61270.18181780.14993387X-RAY DIFFRACTION100
2.6127-2.71710.2091780.15643389X-RAY DIFFRACTION100
2.7171-2.84040.18441790.14743394X-RAY DIFFRACTION100
2.8404-2.98970.2011780.15023377X-RAY DIFFRACTION100
2.9897-3.17630.1811770.14953376X-RAY DIFFRACTION100
3.1763-3.42030.19011790.15193391X-RAY DIFFRACTION100
3.4203-3.76240.16781780.14243392X-RAY DIFFRACTION100
3.7624-4.30190.14231790.13183400X-RAY DIFFRACTION100
4.3019-5.40140.14241800.13173412X-RAY DIFFRACTION100
5.4014-19.71740.17931820.19293446X-RAY DIFFRACTION100

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