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- PDB-1f52: CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMU... -

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Basic information

Entry
Database: PDB / ID: 1f52
TitleCRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM CO-CRYSTALLIZED WITH ADP
ComponentsGLUTAMINE SYNTHETASE
KeywordsLIGASE / glutamine synthetase / ADP / MPD
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 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-5'-DIPHOSPHATE / : / Glutamine synthetase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsGill, H.S. / Pfluegl, G.M.U. / 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
DepositionJun 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2000Provider: 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_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 / _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

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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)630,21472
Polymers620,93312
Non-polymers9,28160
Water63,1253504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area95900 Å2
ΔGint-949 kcal/mol
Surface area172410 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) / Description: 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 / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical...
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3504 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
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: 2.49→34.9 Å / Num. all: 196561 / Num. obs: 196561 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 56.6 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 32.6
Reflection shellResolution: 2.49→2.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.133 / Num. unique all: 8787 / % possible all: 87.8
Reflection
*PLUS

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→34.9 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The model was refined using strict 12-fold NCS-averaging, i.e. constraints. The 2-methyl-2,4-pentanediol (MPD) molecules were restrained to match PDB code 3AL1. A bulk solvent correction was ...Details: The model was refined using strict 12-fold NCS-averaging, i.e. constraints. The 2-methyl-2,4-pentanediol (MPD) molecules were restrained to match PDB code 3AL1. A bulk solvent correction was applied to the data set. Method Used: J.-S. Jiang and A.T. Brunger, J. Mol. Biol. 243, 100-115 (1994).
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1965 -RANDOM
Rwork0.2432 ---
all0.2434 196561 --
obs0.2434 196561 98.2 %-
Displacement parametersBiso mean: 55.54 Å2
Baniso -1Baniso -2Baniso -3
1-32.36 Å20 Å25.866 Å2
2--17.02 Å20 Å2
3---11.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.42 Å
Luzzati d res low-7 Å
Refinement stepCycle: LAST / Resolution: 2.49→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43644 0 348 3696 47688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.82
X-RAY DIFFRACTIONx_dihedral_angle_d24.95
X-RAY DIFFRACTIONx_improper_angle_d1.84
Refine LS restraints NCSNCS model details: CONSTRAINED
Xplor fileSerial no: 1 / Param file: parhcsdx.pro / Topol file: tophcsdx.pro
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 34.9 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.95
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.84

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