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- PDB-1f1h: CRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMU... -

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Basic information

Entry
Database: PDB / ID: 1f1h
TitleCRYSTAL STRUCTURE OF GLUTAMINE SYNTHETASE FROM SALMONELLA TYPHIMURIUM WITH THALLIUM IONS
ComponentsPROTEIN (GLUTAMINE SYNTHETASE)
KeywordsLIGASE / GLUTAMINE SYNTHETASE / THALLIUM IONS
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 / : / THALLIUM (I) ION / Glutamine synthetase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMEN / Resolution: 2.67 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
DepositionMay 19, 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_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_asym_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: PROTEIN (GLUTAMINE SYNTHETASE)
B: PROTEIN (GLUTAMINE SYNTHETASE)
C: PROTEIN (GLUTAMINE SYNTHETASE)
D: PROTEIN (GLUTAMINE SYNTHETASE)
E: PROTEIN (GLUTAMINE SYNTHETASE)
F: PROTEIN (GLUTAMINE SYNTHETASE)
G: PROTEIN (GLUTAMINE SYNTHETASE)
H: PROTEIN (GLUTAMINE SYNTHETASE)
I: PROTEIN (GLUTAMINE SYNTHETASE)
J: PROTEIN (GLUTAMINE SYNTHETASE)
K: PROTEIN (GLUTAMINE SYNTHETASE)
L: PROTEIN (GLUTAMINE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)633,70184
Polymers620,93312
Non-polymers12,76872
Water26,1581452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100370 Å2
ΔGint-988 kcal/mol
Surface area168050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.130, 132.790, 196.780
Angle α, β, γ (deg.)90.00, 102.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
PROTEIN (GLUTAMINE SYNTHETASE)


Mass: 51744.418 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: GRAM NEGATIVE BACTERIA / Source: (natural) Salmonella typhimurium (bacteria) / References: UniProt: P0A1P6, glutamine synthetase

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Non-polymers , 5 types, 1524 molecules

#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-TL / THALLIUM (I) ION / Thallium


Mass: 204.383 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Tl
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1452 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growpH: 7.5
Details: ADP, MPD, SPERMINE, MANGANESE CHLORIDE, IMIDAZOLE BUFFER, pH 7.50
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 31, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.67→32 Å / Num. obs: 268069 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.8
Reflection shellResolution: 2.67→2.8 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.43 / % possible all: 55
Reflection
*PLUS
Highest resolution: 2.67 Å / Lowest resolution: 32 Å / Num. obs: 130547

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMEN / Resolution: 2.67→32 Å / σ(F): 0
Details: THE MODEL WAS REFINED USING STRICT 12-FOLD NCS-AVERAGING, I.E. CONSTRAINTS. THE 2- METHYL-2,4-PENTANEDIOL (MPD) MOLECULE WAS RESTRAINED TO MATCH PD 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) MOLECULE WAS RESTRAINED TO MATCH PD 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
Rfree0.263 6529 -RANDOM
Rwork0.232 ---
obs0.232 130596 82 %-
Displacement parametersBiso mean: 46.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-7 Å
Refinement stepCycle: LAST / Resolution: 2.67→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43644 0 372 1548 45564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.79
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.07
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.81
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
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.67→2.79 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.38 391 4.8 %
Rwork0.35 8079 -
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.07
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.81
LS refinement shell
*PLUS
Rfactor Rfree: 0.38 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.35

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