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- PDB-1lgr: INTERACTIONS OF NUCLEOTIDES WITH FULLY UNADENYLYLATED GLUTAMINE S... -

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Basic information

Entry
Database: PDB / ID: 1lgr
TitleINTERACTIONS OF NUCLEOTIDES WITH FULLY UNADENYLYLATED GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM
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 / metal ion binding / cytoplasm
Similarity search - Function
Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase, N-terminal domain / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain ...Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase, N-terminal domain / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / 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, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / Glutamine synthetase / Glutamine synthetase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.79 Å
AuthorsLiaw, S.-H. / Eisenberg, D.
Citation
Journal: Biochemistry / Year: 1994
Title: Interactions of nucleotides with fully unadenylylated glutamine synthetase from Salmonella typhimurium.
Authors: Liaw, S.H. / Jun, G. / Eisenberg, D.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Refined Atomic Model of Glutamine Synthetase at 3.5 Angstroms Resolution
Authors: Yamashita, M.M. / Almassy, R.J. / Janson, C.A. / Cascio, D. / Eisenberg, D.
#2: 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.
History
DepositionAug 5, 1994Processing site: BNL
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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

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)626,41848
Polymers620,93312
Non-polymers5,48536
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area81790 Å2
ΔGint-581 kcal/mol
Surface area162460 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
Atom site foot note1: CIS PROLINE - PRO 184
2: SER 350 - PRO 351 OMEGA = 218.02 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.50345, 0.85968, -0.08649), (-0.864, 0.50115, -0.04814), (0.00196, 0.09896, 0.995089)-27.9228, -43.9633, -0.0994
2given(-0.4915, 0.85393, -0.1708), (-0.8667, -0.4988, 0.00055), (-0.0847, 0.14827, 0.98531)-79.9279, -41.9148, -4.7344
3given(-0.9853, -0.0089, -0.17101), (-0.0084, -0.9949, 0.100362), (-0.171, 0.10032, 0.980144)-103.823, 4.0715, -9.1552
4given(-0.4898, -0.8677, -0.0848), (0.85485, -0.4971, 0.14868), (-0.1712, 0.0003, 0.98524)-75.9857, 48.0248, -8.8917
5given(0.50423, -0.8636, -0.00092), (0.85948, 0.50173, 0.097734), (-0.0839, -0.0501, 0.995212)-24.1196, 45.8736, -4.1976
6given(0.97771, -0.1161, 0.17494), (-0.116, -0.9932, -0.0107), (0.17499, -0.0099, -0.9845)7.4089, -6.5114, -88.1619
7given(0.59459, 0.79805, 0.09784), (0.7983, -0.6005, 0.046398), (0.09578, 0.05052, -0.99412)-14.5445, 40.1366, -92.4116
8given(-0.3943, 0.91895, 0.00788), (0.91898, 0.39423, 0.00814), (0.00437, 0.01045, -0.9999)-66.5478, 44.4036, -97.0604
9given(-0.9924, 0.12263, -0.00297), (0.1224, 0.98832, -0.09075), (-0.00819, -0.0904, -0.99587)-95.9341, 1.402, -97.516
10given(-0.6113, -0.7879, 0.07386), (-0.7878, 0.59702, -0.1515), (0.07527, -0.1508, -0.9857)-74.1465, -45.3029, -92.9298
11given(0.37841, -0.9111, 0.163623), (-0.9107, -0.398, -0.11006), (0.1654, -0.1074, -0.98037)-22.0703, -49.3726, -88.3892

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Components

#1: Protein
GLUTAMINE SYNTHETASE /


Mass: 51744.418 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
References: UniProt: P06201, UniProt: P0A1P6*PLUS, glutamine synthetase
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mMimidazole hydrochloride1drop
23 mM1dropMn2+
33 mMspermine tetrahydrochloride1drop
410 %MPD1drop
50.05 Mpotassium phosphate-sodium hydroxide1reservoir
62.95 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 99219 / Num. measured all: 146242 / Rmerge(I) obs: 0.066

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.79→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.233 -
obs0.233 99220
Refinement stepCycle: LAST / Resolution: 2.79→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41460 0 300 0 41760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 99220 / Rfactor all: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3

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