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- PDB-1fpy: CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMU... -

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Basic information

Entry
Database: PDB / ID: 1fpy
TitleCRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM WITH INHIBITOR PHOSPHINOTHRICIN
ComponentsGLUTAMINE SYNTHETASE
KeywordsLIGASE / glutamine synthetase / phosphinothricin / inhibition
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 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / 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 / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / 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
ADENOSINE-5'-DIPHOSPHATE / : / PHOSPHINOTHRICIN / Glutamine synthetase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.89 Å
AuthorsGill, H.S. / Eisenberg, D.
CitationJournal: Biochemistry / Year: 2001
Title: The crystal structure of phosphinothricin in the active site of glutamine synthetase illuminates the mechanism of enzymatic inhibition.
Authors: Gill, H.S. / Eisenberg, D.
History
DepositionAug 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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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)629,55160
Polymers620,93312
Non-polymers8,61848
Water33,0761836
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area94800 Å2
ΔGint-546 kcal/mol
Surface area167720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.600, 132.500, 195.900
Angle α, β, γ (deg.)90.00, 102.40, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological complex is a dodecamer.

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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) / Production host: Escherichia coli (E. coli) / 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: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PPQ / PHOSPHINOTHRICIN / 2-AMINO-4-(HYDROXYMETHYL-PHOSPHINYL)BUTANOIC ACID


Mass: 181.127 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H12NO4P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1836 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ADP, MPD, spermine, manganese chloride, imidazole buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mMimidazole/HCl11
23 mM11MnCl2
33 mMspermine tetrahydrochloride11
410 %MPD11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.89→15 Å / Num. all: 87421 / Num. obs: 87421 / % possible obs: 70 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.6 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 13.5
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.288 / Num. unique all: 87421 / % possible all: 58.6
Reflection
*PLUS
% possible obs: 70 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.89→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The model was built using 12-fold NCS averaged maps and refined using (strict) 12-fold NCS-averaging, or constraints. The phosphinothricin model was restrained to match small-molecule ...Details: The model was built using 12-fold NCS averaged maps and refined using (strict) 12-fold NCS-averaging, or constraints. The phosphinothricin model was restrained to match small-molecule structure solutions (see article). Some of the closely spaced waters are most likely a MPD molecule, such as O61 & O28. A BULK SOLVENT CORRECTION and an anisotropic B-factor correction was applied to the data set (see XPLOR 3.843). Alternate conformations B reflect the movements of catalytic loops upon phosphinothricin binding in the active site, whereas alternate conformations A reflect a native structure. See article for details.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 8757 -RANDOM
Rwork0.248 ---
all0.25 87421 --
obs0.25 87421 70 %-
Refinement stepCycle: LAST / Resolution: 2.89→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44964 0 480 1836 47280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_d1.9
X-RAY DIFFRACTIONx_dihedral_angle_d24.88
X-RAY DIFFRACTIONx_improper_angle_d1.81
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.88
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.81

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