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- PDB-1gsh: STRUCTURE OF ESCHERICHIA COLI GLUTATHIONE SYNTHETASE AT PH 7.5 -

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Basic information

Entry
Database: PDB / ID: 1gsh
TitleSTRUCTURE OF ESCHERICHIA COLI GLUTATHIONE SYNTHETASE AT PH 7.5
ComponentsGLUTATHIONE BIOSYNTHETIC LIGASE
KeywordsGLUTATHIONE BIOSYNTHESIS LIGASE / GLUTATHIONE BIOSYNTHESIS / GLUTATHIONE SYNTHASE
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
Glutathione synthetase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsMatsuda, K. / Kato, H. / Yamaguchi, H. / Nishioka, T. / Katsube, Y. / Oda, J.
Citation
Journal: Protein Eng. / Year: 1996
Title: Crystal structure of glutathione synthetase at optimal pH: domain architecture and structural similarity with other proteins.
Authors: Matsuda, K. / Mizuguchi, K. / Nishioka, T. / Kato, H. / Go, N. / 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.Am.Chem.Soc. / Year: 1994
Title: Mechanism-Based Inactivation of Glutathione Synthetase by Phosphinic Acid Transition-State Analogue
Authors: Hiratake, J. / Kato, H. / Oda, J.
#3: Journal: Biochemistry / Year: 1993
Title: Use of Adenosine (5')Polyphospho(5')Pyridoxals to Study the Substrate-Binding Region of Glutathione Synthetase from Escherichia Coli B
Authors: Hibi, T. / Kato, H. / Nishioka, T. / Oda, J. / Yamaguchi, H. / Katsube, Y. / Tanizawa, K. / Fukui, T.
#4: Journal: Biochemistry / Year: 1993
Title: Flexibility Impaired by Mutations Revealed the Multifunctional Roles of the Loop in Glutathione Synthetase
Authors: Tanaka, T. / Yamaguchi, H. / Kato, H. / Nishioka, T. / Katsube, Y. / Oda, J.
#5: 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.
#6: Journal: Photon Factory Activity Report / Year: 1992
Title: Structural Studies on Glutathione Synthetase from Escherichia Coli B
Authors: Yamaguchi, H. / Kato, H. / Hata, Y. / Nishioka, T. / Oda, J. / Katsube, Y.
#7: 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.
History
DepositionMay 16, 1995Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 19, 2014Group: Database references
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONE BIOSYNTHETIC LIGASE


Theoretical massNumber of molelcules
Total (without water)35,6021
Polymers35,6021
Non-polymers00
Water1,72996
1
A: GLUTATHIONE BIOSYNTHETIC LIGASE

A: GLUTATHIONE BIOSYNTHETIC LIGASE

A: GLUTATHIONE BIOSYNTHETIC LIGASE

A: GLUTATHIONE BIOSYNTHETIC LIGASE


Theoretical massNumber of molelcules
Total (without water)142,4074
Polymers142,4074
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)87.800, 87.800, 170.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein GLUTATHIONE BIOSYNTHETIC LIGASE / GLUTATHIONE SYNTHASE


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, A DERIVATIVE OF PKK223-3 / Gene (production host): GSHII / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P04425, glutathione synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.81 Å3/Da / Density % sol: 44 %
Crystal growMethod: microdialysis / pH: 7.5
Details: CRYSTALS WERE PREPARED AT PH 7.5 BY MICRODIALYSIS METHOD WITH AMMONIUM SULFATE AS THE PRECIPITATING AGENT. THE INNER SOLUTION 100 MICROLITER CONTAINED 1.5 % (W/V) GSHASE, 5 MM MGCL2 AND 10 % ...Details: CRYSTALS WERE PREPARED AT PH 7.5 BY MICRODIALYSIS METHOD WITH AMMONIUM SULFATE AS THE PRECIPITATING AGENT. THE INNER SOLUTION 100 MICROLITER CONTAINED 1.5 % (W/V) GSHASE, 5 MM MGCL2 AND 10 % SATURATED AMMONIUM SULFATE IN 50 MM TRIS-HCL BUFFER (PH 7.5). THE INNER SOLUTION WAS DIALYZED AGAINST 50 MM TRIS-HCL BUFFER (PH 7.5) WHICH CONTAINED 5 MM MGCL2 AND 25 % SATURATED AMMONIUM SULFATE.TRIS-HCL BUFFER, microdialysis
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl11
25 mM11MgCl2
325 %satammonium sulfate11

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 18, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 30967 / % possible obs: 90.3 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07
Reflection
*PLUS
Highest resolution: 1.8 Å / % possible obs: 84.1 % / Rmerge(I) obs: 0.0701

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.208 --
obs0.208 24108 90.3 %
Displacement parametersBiso mean: 18.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 96 2465
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_deg2.773
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.35
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.005
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it18.27
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it21.41
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 23.5
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_dihedral_angle_d / Dev ideal: 25.359

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