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- PDB-1m0t: Yeast Glutathione Synthase -

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Basic information

Entry
Database: PDB / ID: 1m0t
TitleYeast Glutathione Synthase
Componentsglutathione synthetase
KeywordsLIGASE / AMINE/CARBOXYLATE LIGASE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Glutathione synthesis and recycling / glutathione synthase / glutathione synthase activity / glutathione biosynthetic process / glutathione binding / magnesium ion binding / protein homodimerization activity / ATP binding / cytoplasm / cytosol
Similarity search - Function
Glutathione synthase lid domain / Dna Ligase; domain 1 - #80 / Glutathione Synthetase; Chain A, domain 3 / Glutathione Synthetase; Chain A, domain 3 / Glutathione synthase, substrate-binding domain superfamily, eukaryotic / Glutathione synthase, substrate-binding domain / Eukaryotic glutathione synthase / Glutathione synthase, alpha-helical / Glutathione synthase, substrate-binding domain superfamily / Glutathione synthase, N-terminal, eukaryotic ...Glutathione synthase lid domain / Dna Ligase; domain 1 - #80 / Glutathione Synthetase; Chain A, domain 3 / Glutathione Synthetase; Chain A, domain 3 / Glutathione synthase, substrate-binding domain superfamily, eukaryotic / Glutathione synthase, substrate-binding domain / Eukaryotic glutathione synthase / Glutathione synthase, alpha-helical / Glutathione synthase, substrate-binding domain superfamily / Glutathione synthase, N-terminal, eukaryotic / Glutathione synthase, C-terminal, eukaryotic / Glutathione synthase / Eukaryotic glutathione synthase, ATP binding domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutathione synthetase GSH2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGogos, A. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Structure / Year: 2002
Title: Large Conformational Changes in the Catalytic Cycle of Glutathione Synthase
Authors: Gogos, A. / Shapiro, L.
History
DepositionJun 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_site
Item: _audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id ..._audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glutathione synthetase
B: glutathione synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,3348
Polymers111,7582
Non-polymers5766
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-89 kcal/mol
Surface area38400 Å2
MethodPISA
2
A: glutathione synthetase
B: glutathione synthetase
hetero molecules

A: glutathione synthetase
B: glutathione synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,66916
Polymers223,5164
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area13480 Å2
ΔGint-196 kcal/mol
Surface area72510 Å2
MethodPISA
3
A: glutathione synthetase
hetero molecules

A: glutathione synthetase
hetero molecules

B: glutathione synthetase
hetero molecules

B: glutathione synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,66916
Polymers223,5164
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
crystal symmetry operation2_554-x,-y,z-1/21
crystal symmetry operation4_556x,-y,-z+11
Buried area7340 Å2
ΔGint-179 kcal/mol
Surface area78640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.869, 155.069, 190.582
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein glutathione synthetase / Glutathione synthase / GSH synthetase / GSH-S


Mass: 55878.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GSH2 / Plasmid: pET28TEV / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q08220, glutathione synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium sulphate, PEG 400, Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
117 mg/mlprotein1drop
210 mMTris-HCl1droppH8.0
3150 mM1dropNaCl
41 mMdithiothreitol1drop
51.97 Mammonium sulfate1reservoir
60.1 MTris-HCl1reservoirpH8.0
72 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 20, 2001
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 45753 / Num. obs: 45753 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 9.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 10.1 / Num. unique all: 4570 / Rsym value: 0.177 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 573251
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HGS

2hgs


Resolution: 2.3→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2301 5.3 %RANDOM
Rwork0.216 ---
all0.216 ---
obs0.216 44565 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 84.6575 Å2 / ksol: 0.442753 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.94 Å20 Å20 Å2
2--10.99 Å20 Å2
3----5.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7451 0 30 498 7979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 399 5.5 %
Rwork0.231 6894 -
obs-6894 95.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. reflection Rfree: 2340 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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