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- PDB-2wgs: Crystal structure of Mycobacterium Tuberculosis Glutamine Synthet... -

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Basic information

Entry
Database: PDB / ID: 2wgs
TitleCrystal structure of Mycobacterium Tuberculosis Glutamine Synthetase in complex with a purine analogue inhibitor.
ComponentsGLUTAMINE SYNTHETASE 1
KeywordsLIGASE / RELAXED STATE / PURINE ANALOGUE / NUCLEOTIDE-BINDING / GLNA1 / MT2278 / RV2220 / CYTOPLASM / SYNTHETASE
Function / homology
Function and homology information


nitrogen utilization / positive regulation of plasminogen activation / cell wall / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / fibronectin binding / peptidoglycan-based cell wall / protein homooligomerization ...nitrogen utilization / positive regulation of plasminogen activation / cell wall / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / zymogen binding / fibronectin binding / peptidoglycan-based cell wall / protein homooligomerization / magnesium ion binding / extracellular region / ATP binding / metal ion binding / membrane / plasma membrane / cytosol / 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
Chem-1AZ / Glutamine synthetase / Glutamine synthetase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsNilsson, M.T. / Krajewski, W.W. / Jones, T.A. / Mowbray, S.L.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Structural Basis for the Inhibition of Mycobacterium Tuberculosis Glutamine Synthetase by Novel ATP-Competitive Inhibitors.
Authors: Nilsson, M.T. / Krajewski, W.W. / Yellagunda, S. / Prabhumurthy, S. / Chamarahally, G.N. / Siddamadappa, C. / Srinivasa, B.R. / Yahiaoui, S. / Larhed, M. / Karlen, A. / Jones, T.A. / Mowbray, S.L.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of Mycobacterium Tuberculosis Glutamine Synthetase in Complex with a Transition-State Mimic Provides Functional Insights.
Authors: Krajewski, W.W. / Jones, T.A. / Mowbray, S.L.
History
DepositionApr 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTAMINE SYNTHETASE 1
B: GLUTAMINE SYNTHETASE 1
C: GLUTAMINE SYNTHETASE 1
D: GLUTAMINE SYNTHETASE 1
E: GLUTAMINE SYNTHETASE 1
F: GLUTAMINE SYNTHETASE 1
G: GLUTAMINE SYNTHETASE 1
H: GLUTAMINE SYNTHETASE 1
I: GLUTAMINE SYNTHETASE 1
J: GLUTAMINE SYNTHETASE 1
K: GLUTAMINE SYNTHETASE 1
L: GLUTAMINE SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)660,53436
Polymers655,01712
Non-polymers5,51724
Water27,6711536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area85650 Å2
ΔGint-553.61 kcal/mol
Surface area183690 Å2
MethodPISA
2
A: GLUTAMINE SYNTHETASE 1
B: GLUTAMINE SYNTHETASE 1
C: GLUTAMINE SYNTHETASE 1
D: GLUTAMINE SYNTHETASE 1
E: GLUTAMINE SYNTHETASE 1
F: GLUTAMINE SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,26718
Polymers327,5086
Non-polymers2,75812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23490 Å2
ΔGint-158.76 kcal/mol
Surface area111190 Å2
MethodPISA
3
G: GLUTAMINE SYNTHETASE 1
H: GLUTAMINE SYNTHETASE 1
I: GLUTAMINE SYNTHETASE 1
J: GLUTAMINE SYNTHETASE 1
K: GLUTAMINE SYNTHETASE 1
L: GLUTAMINE SYNTHETASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,26718
Polymers327,5086
Non-polymers2,75812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23500 Å2
ΔGint-159.07 kcal/mol
Surface area111170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.950, 203.180, 230.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A4 - 728
2111B4 - 728
3111C4 - 728
4111D4 - 728
5111E4 - 728
6111F4 - 728
7111G4 - 728
8111H4 - 728
9111I4 - 728
10111J4 - 728
11111K4 - 728
12111L4 - 728

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Components

#1: Protein
GLUTAMINE SYNTHETASE 1 / GLUTAMATE--AMMONIA LIGASE 1


Mass: 54584.730 Da / Num. of mol.: 12 / Fragment: RESIDUES 2-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV
Description: E. COLI STRAIN GJ4745 IS ADENYLYLTRANSFERASE DEFICIENT (GLNE-)
Plasmid: PTRC99C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GJ4745
References: UniProt: P0A590, UniProt: P9WN39*PLUS, glutamine synthetase
#2: Chemical
ChemComp-1AZ / 1-(3,4-dichlorobenzyl)-3,7-dimethyl-8-morpholin-4-yl-3,7-dihydro-1H-purine-2,6-dione


Mass: 424.281 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C18H19Cl2N5O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1536 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN EXPRESSED IN FUSION WITH A N-TERMINAL 9 AMINO ACID PEPTIDE CONTAINING A SIX HISTIDINE ...PROTEIN EXPRESSED IN FUSION WITH A N-TERMINAL 9 AMINO ACID PEPTIDE CONTAINING A SIX HISTIDINE PURIFICATION TAG.

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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: 2.43 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M SODIUM ACETATE, PH 5, 0.75 M 1,6-HEXANEDIOL) AND PROTEIN SOLUTION (10 G/L IN 0.020 M TRIS-HCL. PH 7.5, 0.15 M SODIUM CHLORIDE, 0.005 M MAGNESIUM ...Details: EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M SODIUM ACETATE, PH 5, 0.75 M 1,6-HEXANEDIOL) AND PROTEIN SOLUTION (10 G/L IN 0.020 M TRIS-HCL. PH 7.5, 0.15 M SODIUM CHLORIDE, 0.005 M MAGNESIUM CHLORIDE, 2%(V/V) DMSO, 0.0002 M INHIBITOR), VAPOR DIFFUSION, HANGING-DROP, TEMPERATURE 294K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.55→29.9 Å / Num. obs: 200628 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.3
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.8 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HTO

1hto


Resolution: 2.55→29.95 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.94 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 1.195 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AMINO ACIDS 63 TO 66 AND 405 TO 412 WERE OMITTED FROM THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.24586 10318 5 %RANDOM
Rwork0.2302 ---
obs0.23098 194667 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.987 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20 Å2
2--1.62 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43920 0 348 1536 45804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02245492
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.221.9661836
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62855520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47924.1182244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.359157044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.83815252
X-RAY DIFFRACTIONr_chiral_restr0.0850.26432
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0235832
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.219991
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.231023
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.22360
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5150.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6841.528229
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.229244616
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.223319929
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0544.517220
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3817 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.040.05
4Dtight positional0.030.05
5Etight positional0.040.05
6Ftight positional0.040.05
7Gtight positional0.040.05
8Htight positional0.040.05
9Itight positional0.040.05
10Jtight positional0.040.05
11Ktight positional0.040.05
12Ltight positional0.040.05
1Atight thermal0.070.5
2Btight thermal0.070.5
3Ctight thermal0.080.5
4Dtight thermal0.080.5
5Etight thermal0.080.5
6Ftight thermal0.090.5
7Gtight thermal0.080.5
8Htight thermal0.080.5
9Itight thermal0.080.5
10Jtight thermal0.110.5
11Ktight thermal0.090.5
12Ltight thermal0.090.5
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 738 -
Rwork0.327 14245 -
obs--99.96 %

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