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- PDB-4xyc: NANOMOLAR INHIBITORS OF MYCOBACTERIUM TUBERCULOSIS GLUTAMINE SYNT... -

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Basic information

Entry
Database: PDB / ID: 4xyc
TitleNANOMOLAR INHIBITORS OF MYCOBACTERIUM TUBERCULOSIS GLUTAMINE SYNTHETASE 1: SYNTHESIS, BIOLOGICAL EVALUATION AND X-RAY CRYSTALLOGRAPHIC STUDIES
ComponentsGlutamine synthetase 1
KeywordsLIGASE/LIGASE INHIBITOR / LIGASE / ATP BINDING / LIGASE-LIGASE INHIBITOR COMPLEX
Function / homology
Function and homology information


glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / : / ATP binding / 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, 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 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, 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
Chem-2K9 / Glutamine synthetase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsCouturier, C. / Silve, S. / Morales, R. / Ppessegue, B. / Llopart, S. / Nair, A. / Bauer, A. / Scheiper, B. / poeverlein, c. / Ganzhorn, A. ...Couturier, C. / Silve, S. / Morales, R. / Ppessegue, B. / Llopart, S. / Nair, A. / Bauer, A. / Scheiper, B. / poeverlein, c. / Ganzhorn, A. / Lagrange, S. / Bacque, E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Nanomolar inhibitors of Mycobacterium tuberculosis glutamine synthetase 1: Synthesis, biological evaluation and X-ray crystallographic studies.
Authors: Couturier, C. / Silve, S. / Morales, R. / Pessegue, B. / Llopart, S. / Nair, A. / Bauer, A. / Scheiper, B. / Poverlein, C. / Ganzhorn, A. / Lagrange, S. / Bacque, E.
History
DepositionFeb 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
M: Glutamine synthetase 1
N: Glutamine synthetase 1
O: Glutamine synthetase 1
P: Glutamine synthetase 1
Q: Glutamine synthetase 1
R: Glutamine synthetase 1
S: Glutamine synthetase 1
T: Glutamine synthetase 1
U: Glutamine synthetase 1
V: Glutamine synthetase 1
W: Glutamine synthetase 1
X: Glutamine synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,294,20148
Polymers1,287,06524
Non-polymers7,13524
Water0
1
A: Glutamine synthetase 1
B: Glutamine synthetase 1
C: Glutamine synthetase 1
D: Glutamine synthetase 1
E: Glutamine synthetase 1
F: Glutamine synthetase 1
M: Glutamine synthetase 1
N: Glutamine synthetase 1
O: Glutamine synthetase 1
P: Glutamine synthetase 1
Q: Glutamine synthetase 1
R: Glutamine synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)647,10024
Polymers643,53312
Non-polymers3,56812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80280 Å2
ΔGint-420 kcal/mol
Surface area189720 Å2
MethodPISA
2
G: Glutamine synthetase 1
H: Glutamine synthetase 1
I: Glutamine synthetase 1
J: Glutamine synthetase 1
K: Glutamine synthetase 1
L: Glutamine synthetase 1
S: Glutamine synthetase 1
T: Glutamine synthetase 1
U: Glutamine synthetase 1
V: Glutamine synthetase 1
W: Glutamine synthetase 1
X: Glutamine synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)647,10024
Polymers643,53312
Non-polymers3,56812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area79680 Å2
ΔGint-429 kcal/mol
Surface area190020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)260.112, 273.497, 207.634
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
11B
21A
12C
22A
13D
23A
14E
24A
15F
25A
16G
26A
17H
27A
18I
28A
19J
29A
110K
210A
111L
211A
112M
212A
113N
213A
114O
214A
115P
215A
116Q
216A
117R
217A
118S
218A
119T
219A
120U
220A
121V
221A
122W
222A
123X
223A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B0 - 474
2114A0 - 474
1124C0 - 474
2124A0 - 474
1134D0 - 474
2134A0 - 474
1144E0 - 474
2144A0 - 474
1154F0 - 474
2154A0 - 474
1164G0 - 474
2164A0 - 474
1174H0 - 474
2174A0 - 474
1184I0 - 474
2184A0 - 474
1194J0 - 474
2194A0 - 474
11104K0 - 474
21104A0 - 474
11114L0 - 474
21114A0 - 474
11124M0 - 474
21124A0 - 474
11134N0 - 474
21134A0 - 474
11144O0 - 474
21144A0 - 474
11154P0 - 474
21154A0 - 474
11164Q0 - 474
21164A0 - 474
11174R0 - 474
21174A0 - 474
11184S0 - 474
21184A0 - 474
11194T0 - 474
21194A0 - 474
11204U0 - 474
21204A0 - 474
11214V0 - 474
21214A0 - 474
11224W0 - 474
21224A0 - 474
11234X0 - 474
21234A0 - 474

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23

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Components

#1: Protein ...
Glutamine synthetase 1 / / Glutamate--ammonia ligase 1


Mass: 53627.727 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glnA1, glnA, MT2278 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLyss / References: UniProt: P9WN38, glutamine synthetase
#2: Chemical...
ChemComp-2K9 / 9-phenyl-4H-imidazo[1,2-a]indeno[1,2-e]pyrazin-4-one


Mass: 297.310 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C19H11N3O

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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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24% PEG3350, 0.2 M KSCN, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
PH range: 7.5

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 221564 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 9.3
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WGS

2wgs


Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.868 / SU B: 27.428 / SU ML: 0.447 / Cross valid method: FREE R-VALUE / σ(F): 1 / ESU R Free: 0.58 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 11105 5 %RANDOM
Rwork0.2 ---
obs0.203 210213 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.52 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å20 Å2
2---1.66 Å20 Å2
3---4.3 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms88296 0 552 0 88848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02291424
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.962124404
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.807511096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24824.2734540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.6591514124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.95315480
X-RAY DIFFRACTIONr_chiral_restr0.0880.212952
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02172312
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6221.555676
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.165289760
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.995335748
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8284.534644
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

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B3670medium positional0.280.5
2C3645medium positional0.260.5
3D3674medium positional0.230.5
4E3670medium positional0.260.5
5F3693medium positional0.280.5
6G3693medium positional0.210.5
7H3670medium positional0.280.5
8I3645medium positional0.240.5
9J3674medium positional0.240.5
10K3670medium positional0.250.5
11L3693medium positional0.230.5
12M3693medium positional0.220.5
13N3670medium positional0.250.5
14O3645medium positional0.240.5
15P3674medium positional0.240.5
16Q3670medium positional0.250.5
17R3693medium positional0.240.5
18S3693medium positional0.230.5
19T3670medium positional0.250.5
20U3645medium positional0.220.5
21V3674medium positional0.220.5
22W3670medium positional0.240.5
23X3693medium positional0.240.5
1B3670medium thermal0.922
2C3645medium thermal0.692
3D3674medium thermal1.092
4E3670medium thermal12
5F3693medium thermal0.752
6G3693medium thermal0.682
7H3670medium thermal0.72
8I3645medium thermal0.732
9J3674medium thermal1.032
10K3670medium thermal0.842
11L3693medium thermal0.722
12M3693medium thermal0.672
13N3670medium thermal0.712
14O3645medium thermal0.672
15P3674medium thermal0.692
16Q3670medium thermal0.892
17R3693medium thermal0.752
18S3693medium thermal0.72
19T3670medium thermal0.662
20U3645medium thermal0.72
21V3674medium thermal0.882
22W3670medium thermal0.72
23X3693medium thermal0.922

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