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- PDB-1gsa: STRUCTURE OF GLUTATHIONE SYNTHETASE COMPLEXED WITH ADP AND GLUTATHIONE -

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Basic information

Entry
Database: PDB / ID: 1gsa
TitleSTRUCTURE OF GLUTATHIONE SYNTHETASE COMPLEXED WITH ADP AND GLUTATHIONE
ComponentsGLUTATHIONE SYNTHETASE
KeywordsLIGASE / GLUTATHIONE SYNTHETASE
Function / homology
Function and homology information


glutathione synthase / glutathione synthase activity / glutathione biosynthetic process / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Prokaryotic glutathione synthetase, N-terminal / Glutathione synthetase, prokaryotic / Prokaryotic glutathione synthetase, N-terminal domain / Prokaryotic glutathione synthetase, ATP-binding / Prokaryotic glutathione synthetase, ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily ...Prokaryotic glutathione synthetase, N-terminal / Glutathione synthetase, prokaryotic / Prokaryotic glutathione synthetase, N-terminal domain / Prokaryotic glutathione synthetase, ATP-binding / Prokaryotic glutathione synthetase, ATP-grasp domain / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GLUTATHIONE / Glutathione synthetase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsHara, T. / Kato, H. / Nishioka, T. / Katsube, Y. / Oda, J.
Citation
Journal: Biochemistry / Year: 1996
Title: A pseudo-michaelis quaternary complex in the reverse reaction of a ligase: structure of Escherichia coli B glutathione synthetase complexed with ADP, glutathione, and sulfate at 2.0 A resolution.
Authors: Hara, T. / Kato, H. / Katsube, Y. / Oda, J.
#1: Journal: Biochemistry / Year: 1994
Title: Flexible Loop that is Novel Catalytic Machinery in a Ligase. Atomic Structure and Function of the Loopless Glutathione Synthetase
Authors: Kato, H. / Tanaka, T. / Yamaguchi, H. / Hara, T. / Nishioka, T. / Katsube, Y. / Oda, J.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Three-Dimensional Structure of the Glutathione Synthetase from Escherichia Coli B at 2.0 A Resolution
Authors: Yamaguchi, H. / Kato, H. / Hata, Y. / Nishioka, T. / Kimura, A. / Oda, J. / Katsube, Y.
#3: Journal: Agric.Biol.Chem. / Year: 1989
Title: Overexpression of Glutathione Synthetase in Escherichia Coli
Authors: Kato, H. / Kobayashi, M. / Murata, K. / Nishioka, T. / Oda, J.
#4: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallization and Preliminary X-Ray Studies of Glutathione Synthetase from Escherichia Coli B
Authors: Kato, H. / Yamaguchi, H. / Hata, Y. / Nishioka, T. / Katsube, Y. / Oda, J.
#5: Journal: J.Biol.Chem. / Year: 1988
Title: Role of Cysteine Residues in Glutathione Synthetase from Escherichia Coli B. Chemical Modification and Oligonucleotide Site-Directed Mutagenesis
Authors: Kato, H. / Tanaka, T. / Nishioka, T. / Kimura, A. / Oda, J.
History
DepositionJun 8, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4816
Polymers35,6021
Non-polymers8795
Water2,432135
1
A: GLUTATHIONE SYNTHETASE
hetero molecules

A: GLUTATHIONE SYNTHETASE
hetero molecules

A: GLUTATHIONE SYNTHETASE
hetero molecules

A: GLUTATHIONE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,92424
Polymers142,4074
Non-polymers3,51720
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
MethodPQS
2
A: GLUTATHIONE SYNTHETASE
hetero molecules

A: GLUTATHIONE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,96212
Polymers71,2042
Non-polymers1,75810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area7590 Å2
ΔGint-126 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.250, 87.250, 169.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GLUTATHIONE SYNTHETASE / GAMMA-L-GLUTAMYL-L-CYSTEINE\:GLYCINE LIGASE (ADP-FORMING)


Mass: 35601.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: B / Plasmid: PKGS00, AN DERIVATIVE PLASMID OF PKK233-3 / Gene (production host): GSHII / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P04425, glutathione synthase

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Non-polymers , 5 types, 140 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.5
Details: CRYSTALLIZED IN TRIS-HCL BUFFER (PH 7.5). AMMONIUM SULFATE WAS USED AS PRECIPITANT.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl11
225 %satammonium sulfate11
35 mM11MgCl2
410 mM2-mercaptoethanol11
50.02 %11NaN3

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04
DetectorDetector: FILM / Date: Nov 28, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.8→45.1 Å / Num. obs: 23410 / % possible obs: 81.5 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.058
Reflection
*PLUS
Num. measured all: 196511

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
WEISdata reduction
X-PLOR3phasing
RefinementResolution: 2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.188 --
obs0.188 19832 78.9 %
Displacement parametersBiso mean: 19.61 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 54 135 2668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.75
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.43
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARAM19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.79
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.43

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