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- PDB-2gls: REFINED ATOMIC MODEL OF GLUTAMINE SYNTHETASE AT 3.5 ANGSTROMS RES... -

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Basic information

Entry
Database: PDB / ID: 2gls
TitleREFINED ATOMIC MODEL OF GLUTAMINE SYNTHETASE AT 3.5 ANGSTROMS RESOLUTION
ComponentsGLUTAMINE SYNTHETASE
KeywordsLIGASE(AMIDE SYNTHETASE)
Function / homology
Function and homology information


nitrogen utilization / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / protein homooligomerization / manganese ion binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Glutamine synthetase, N-terminal domain / Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, glycine-rich site ...Glutamine synthetase, N-terminal domain / Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Glutamine synthetase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsEisenberg, D. / Almassy, R.J. / Yamashita, M.M.
Citation
Journal: J.Biol.Chem. / Year: 1989
Title: Refined atomic model of glutamine synthetase at 3.5 A resolution.
Authors: Yamashita, M.M. / Almassy, R.J. / Janson, C.A. / Cascio, D. / Eisenberg, D.
#1: Journal: Nature / Year: 1986
Title: Novel Subunit-Subunit Interactions in the Structure of Glutamine Synthetase
Authors: Almassy, R.J. / Janson, C.A. / Hamlin, R. / Xuong, N.-H. / Eisenberg, D.
#2: Journal: Gene / Year: 1986
Title: Sequence of Glutamine Synthetase from Salmonella Typhimurium and Implications for the Protein Structure
Authors: Janson, C.A. / Kayne, P.S. / Almassy, R.J. / Grunstein, M. / Eisenberg, D.
History
DepositionMay 19, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _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
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMINE SYNTHETASE
B: GLUTAMINE SYNTHETASE
C: GLUTAMINE SYNTHETASE
D: GLUTAMINE SYNTHETASE
E: GLUTAMINE SYNTHETASE
F: GLUTAMINE SYNTHETASE
G: GLUTAMINE SYNTHETASE
H: GLUTAMINE SYNTHETASE
I: GLUTAMINE SYNTHETASE
J: GLUTAMINE SYNTHETASE
K: GLUTAMINE SYNTHETASE
L: GLUTAMINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)623,82636
Polymers622,50712
Non-polymers1,31924
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area73600 Å2
ΔGint-552 kcal/mol
Surface area183980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.500, 134.500, 200.100
Angle α, β, γ (deg.)90.00, 102.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GLUTAMINE SYNTHETASE


Mass: 51875.609 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / References: UniProt: P0A1P6, glutamine synthetase
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.1 / Method: vapor diffusion, hanging drop / Details: took from Jonson et al.,(1984) from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mMimidazole1drop
21.1 mM1dropMnCl2
31 mMMPD1drop
41 mMspermine tetrachloride1drop
55 %MPD1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.5 Å / Num. all: 76889 / Num. obs: 65223 / Rmerge F obs: 0.055

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.258 / Highest resolution: 3.5 Å / σ(F): 2
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43632 0 24 36 43692
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0270.02
X-RAY DIFFRACTIONp_angle_d0.040.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0720.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.3151
X-RAY DIFFRACTIONp_mcangle_it0.5222
X-RAY DIFFRACTIONp_scbond_it0.6841
X-RAY DIFFRACTIONp_scangle_it1.182
X-RAY DIFFRACTIONp_plane_restr0.0250.02
X-RAY DIFFRACTIONp_chiral_restr0.3820.15
X-RAY DIFFRACTIONp_singtor_nbd0.2950.5
X-RAY DIFFRACTIONp_multtor_nbd0.4130.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.33
X-RAY DIFFRACTIONp_staggered_tor30.615
X-RAY DIFFRACTIONp_orthonormal_tor35.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 65223 / Rfactor obs: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25 Å2

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