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- PDB-1glv: THREE-DIMENSIONAL STRUCTURE OF THE GLUTATHIONE SYNTHETASE FROM ES... -

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Basic information

Entry
Database: PDB / ID: 1glv
TitleTHREE-DIMENSIONAL STRUCTURE OF THE GLUTATHIONE SYNTHETASE FROM ESCHERICHIA COLI B AT 2.0 ANGSTROMS RESOLUTION
ComponentsGLUTATHIONE SYNTHASE
KeywordsGLUTATHIONE 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, 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 / Resolution: 2.7 Å
AuthorsYamaguchi, H. / Kato, H. / Tanaka, T. / Katsube, Y.
Citation
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.
#1: 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.
#2: 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.
#3: 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
DepositionMar 12, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED *S1* AND *S2*. STRANDS 1 AND 2 ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTATHIONE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)34,2351
Polymers34,2351
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.700, 87.700, 169.850
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 0.829 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: MET 1 EXISTS IN TWO CONFORMATIONS.
DetailsTHE ASYMMETRIC UNIT OF THE CRYSTAL CONTAINS ONE SUBUNIT OF THE TETRAMERIC MOLECULE. SUBUNITS IN THE TETRAMERIC MOLECULE CAN BE GENERATED BY APPLYING FOLLOWING OPERATIONS TO THE FRACTIONAL CRYSTALLOGRAPHIC COORDINATES XFRAC, YFRAC, ZFRAC. 0 1 0 XFRAC 0 XFRAC2 1 0 0 X YFRAC + 0 = YFRAC2 0 0 -1 ZFRAC 0.6666666 ZFRAC2 -1 0 0 XFRAC 1 XFRAC3 0 -1 0 X YFRAC + 1 = XFRAC3 0 0 1 ZFRAC 0 XFRAC3 0 -1 0 XFRAC 1 XFRAC4 -1 0 0 X YFRAC + 1 = YFRAC4 0 0 -1 ZFRAC 0.6666666 ZFRAC4

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Components

#1: Protein GLUTATHIONE SYNTHASE


Mass: 34235.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P04425, glutathione synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE LOOP REGION FROM ILE 226 TO ARG 241 IN THE WILD TYPE ENZYME WERE REPLACED WITH THREE GLY ...THE LOOP REGION FROM ILE 226 TO ARG 241 IN THE WILD TYPE ENZYME WERE REPLACED WITH THREE GLY RESIDUES, GLY 226, GLY 227 AND GLY 228. GLY 228 CONNECTS WITH GLY 242.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: microdialysis / pH: 5.5 / Details: referred to J.Mol.Biol. 209.503-504
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11
22 %(w/v)glutathione synthetase11
320 %satammonium sulfate11
45 mM11MgCl2
550 mMpotassium phosphate11
627 %satammonium sulfate12
75 mM12MgCl2
80.02 %(w/v)12NaN3
950 mMpotassium phosphate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 10757 / % possible obs: 98.3 % / Num. measured all: 32629 / Rmerge(I) obs: 0.033

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.7→6 Å / σ(F): 2 /
RfactorNum. reflection
obs0.177 9009
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 0 18 2407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 6 Å / Num. reflection obs: 9009 / σ(F): 2 / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.030.041
X-RAY DIFFRACTIONp_plane_restr0.020.023
X-RAY DIFFRACTIONp_chiral_restr0.150.176
X-RAY DIFFRACTIONp_mcbond_it22.62
X-RAY DIFFRACTIONp_scbond_it34.68
X-RAY DIFFRACTIONp_mcangle_it33.62
X-RAY DIFFRACTIONp_scangle_it46.16

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