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- PDB-2glt: STRUCTURE OF ESCHERICHIA COLI GLUTATHIONE SYNTHETASE AT PH 6.0. -

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Basic information

Entry
Database: PDB / ID: 2glt
TitleSTRUCTURE OF ESCHERICHIA COLI GLUTATHIONE SYNTHETASE AT PH 6.0.
ComponentsGLUTATHIONE BIOSYNTHETIC LIGASE
KeywordsBIOSYNTHESIS / LIGASE / GLUTATHIONE BIOSYNTHESIS LIGASE
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, subdomain 1 / ATP-grasp fold, B domain / 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, subdomain 1 / ATP-grasp fold, B domain / 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: 2.2 Å
AuthorsMatsuda, K. / Yamaguchi, H. / Kato, 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 Multi-Functional 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 Angstroms Resolution
Authors: Yamaguchi, H. / Kato, H. / Hata, Y. / Nishioka, T. / Kimura, A. / Oda, J. / Katsube, Y.
#6: Journal: Bull.Inst.Chem.Res.,Kyoto Univ. / Year: 1993
Title: Construction, Expression, and Characterization of Glutathione Synthetase Chimeras: Substitution of a Homologous Loop Peptide Region of Dihydrofolate Reductase
Authors: Tanaka, T. / Sakai, T. / Chihara-Siomi, M. / Takeshima, K. / Kato, H. / Misawa, T. / Nishioka, T. / Oda, J.
#7: Journal: Biochemistry / Year: 1992
Title: Mutational and Proteolytic Studies on a Flexible Loop in Glutathione Synthetase from Escherichia Coli B: The Loop and Arginine 233 are Critical for the Catalytic Reaction
Authors: Tanaka, T. / Kato, H. / Nishioka, T. / Oda, J.
#8: 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.
#9: 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.
#10: Journal: Agric.Biol.Chem. / Year: 1989
Title: Overexpression of Glutathione Synthase in Escherichia Coli
Authors: Kato, H. / Kobayashi, M. / Murata, K. / Nishioka, T. / Oda, J.
#11: Journal: J.Biol.Chem. / Year: 1988
Title: Role of Cysteine Residues in Glutathione Synthetase from Escherchia Coli B
Authors: Kato, H. / Tanaka, T. / Nishioka, T. / Kimura, A. / Oda, J.
#12: Journal: Nucleic Acids Res. / Year: 1984
Title: Complete Nucleotide Sequence of E.Coli Glutathione Synthetase Gsh-II
Authors: Gushima, H. / Yasuda, S. / Soeda, E. / Yokota, M. / Kondo, M. / Kimura, A.
History
DepositionMay 16, 1995Processing site: BNL
SupersessionJul 31, 1995ID: 1GLT
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 12, 2014Group: Other
Revision 1.4May 31, 2023Group: Data collection / Database references / Other / Category: database_2 / pdbx_database_status / reflns
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.pdbx_Rmerge_I_obs
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
Water1,65792
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 operation4_665-x+1,-y+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
Unit cell
Length a, b, c (Å)88.000, 88.000, 164.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Atom site foot note1: CIS PROLINE - PRO 90
2: VAL 113 - ASN 114 OMEGA = 357.86 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 1 .. 316 SYMMETRY1 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 0.66667 SYMMETRY1 2 -1.000000 0.000000 0.000000 1.00000 SYMMETRY2 2 0.000000 -1.000000 0.000000 1.00000 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000 SYMMETRY1 3 0.000000 -1.000000 0.000000 1.00000 SYMMETRY2 3 -1.000000 0.000000 0.000000 1.00000 SYMMETRY3 3 0.000000 0.000000 -1.000000 0.66667

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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 / Gene: GSHII / Plasmid: PKGS00 A DERIVATIVE OF / Gene (production host): GSHII / References: UniProt: P04425, glutathione synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.58 Å3/Da / Density % sol: 52.26 %
Description: INTENSITY DATA WERE COLLECTED WITH A WEISSENBERG CAMERA EQUIPPED WITH A CYLINDRICAL CASSETTE HAVING A 430 MM RADIUS AND THE FUJI FILM IMAGING PLATES
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 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Aug 3, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.2→77.8 Å / Num. obs: 24571 / % possible obs: 84.1 % / Observed criterion σ(I): 1
Reflection
*PLUS
% possible obs: 77.8 % / Rmerge(I) obs: 0.053

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.2→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.26 -10 %
Rwork0.202 --
obs0.202 16442 79.8 %
Displacement parametersBiso mean: 21.49 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 92 2461
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.15
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.918
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.65
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.149

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