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

Basic information

• Entry: Database: PDB / ID: 4xyc
• Title: NANOMOLAR INHIBITORS OF MYCOBACTERIUM TUBERCULOSIS GLUTAMINE SYNTHETASE 1: SYNTHESIS, BIOLOGICAL EVALUATION AND X-RAY CRYSTALLOGRAPHIC STUDIES
• Components: Glutamine synthetase 1
• Keywords: LIGASE/LIGASE INHIBITOR / LIGASE / ATP BINDING / LIGASE-LIGASE INHIBITOR COMPLEX

Function / homology

Function:

glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / metal ion binding / cytoplasm

Domain/homology:

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 (GS) beta-grasp domain profile. / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal 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

Component:

Chem-2K9 / Glutamine synthetase

• Biological species: Mycobacterium tuberculosis (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
• Authors: Couturier, C. / Silve, S. / Morales, R. / Ppessegue, B. / Llopart, S. / Nair, A. / Bauer, A. / Scheiper, B. / poeverlein, c. / Ganzhorn, A. / Lagrange, S. / Bacque, E.
• Citation: Journal: 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

Deposition	Feb 2, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 1, 2015	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: 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

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

Summary:

• 1.29 MDa, 24 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	1,294,201	48
Polymers	1,287,065	24
Non-polymers	7,135	24
Water	0	0

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

Summary:

• defined by author&software
• 647 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	647,100	24
Polymers	643,533	12
Non-polymers	3,568	12
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	80280 Å2
ΔGint	-420 kcal/mol
Surface area	189720 Å2
Method	PISA

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

Summary:

• defined by author&software
• 647 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	647,100	24
Polymers	643,533	12
Non-polymers	3,568	12
Water	0

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Calculated values:

Buried area	79680 Å2
ΔGint	-429 kcal/mol
Surface area	190020 Å2
Method	PISA

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 number	19
Space group name H-M	P212121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	B
2	1	A
1	2	C
2	2	A
1	3	D
2	3	A
1	4	E
2	4	A
1	5	F
2	5	A
1	6	G
2	6	A
1	7	H
2	7	A
1	8	I
2	8	A
1	9	J
2	9	A
1	10	K
2	10	A
1	11	L
2	11	A
1	12	M
2	12	A
1	13	N
2	13	A
1	14	O
2	14	A
1	15	P
2	15	A
1	16	Q
2	16	A
1	17	R
2	17	A
1	18	S
2	18	A
1	19	T
2	19	A
1	20	U
2	20	A
1	21	V
2	21	A
1	22	W
2	22	A
1	23	X
2	23	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	B	0 - 474
2	1	1	4	A	0 - 474
1	1	2	4	C	0 - 474
2	1	2	4	A	0 - 474
1	1	3	4	D	0 - 474
2	1	3	4	A	0 - 474
1	1	4	4	E	0 - 474
2	1	4	4	A	0 - 474
1	1	5	4	F	0 - 474
2	1	5	4	A	0 - 474
1	1	6	4	G	0 - 474
2	1	6	4	A	0 - 474
1	1	7	4	H	0 - 474
2	1	7	4	A	0 - 474
1	1	8	4	I	0 - 474
2	1	8	4	A	0 - 474
1	1	9	4	J	0 - 474
2	1	9	4	A	0 - 474
1	1	10	4	K	0 - 474
2	1	10	4	A	0 - 474
1	1	11	4	L	0 - 474
2	1	11	4	A	0 - 474
1	1	12	4	M	0 - 474
2	1	12	4	A	0 - 474
1	1	13	4	N	0 - 474
2	1	13	4	A	0 - 474
1	1	14	4	O	0 - 474
2	1	14	4	A	0 - 474
1	1	15	4	P	0 - 474
2	1	15	4	A	0 - 474
1	1	16	4	Q	0 - 474
2	1	16	4	A	0 - 474
1	1	17	4	R	0 - 474
2	1	17	4	A	0 - 474
1	1	18	4	S	0 - 474
2	1	18	4	A	0 - 474
1	1	19	4	T	0 - 474
2	1	19	4	A	0 - 474
1	1	20	4	U	0 - 474
2	1	20	4	A	0 - 474
1	1	21	4	V	0 - 474
2	1	21	4	A	0 - 474
1	1	22	4	W	0 - 474
2	1	22	4	A	0 - 474
1	1	23	4	X	0 - 474
2	1	23	4	A	0 - 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

Components

#1: Protein

A B C D E F G H I J K L M N O P Q R S ...
Glutamine synthetase 1 / Glutamate--ammonia ligase 1

Details:

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

A-900 B-900 C-900 D-900 E-900 F-900 G-900 H-900 I-900 J-900 K-900 L-900 M-900 N-900 O-900 P-900 Q-900 R-900 S-900 T-900 ...
ChemComp-2K9 / 9-phenyl-4H-imidazo[1,2-a]indeno[1,2-e]pyrazin-4-one

Details:

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

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.87 ų/Da / Density % sol: 57.13 %
• Crystal grow: Temperature: 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

Data collection

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

Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
AMoRE		phasing
REFMAC	5.5.0109	refinement

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WGS

2wgs

Resolution: 3.3→50 Å / Cor.coef. F_o:F_c: 0.928 / Cor.coef. F_o:F_c 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

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.265	11105	5 %	RANDOM
Rwork	0.2	-	-	-
obs	0.203	210213	99.8 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 57.52 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-2.64 Å2	0 Å2	0 Å2
2-	-	-1.66 Å2	0 Å2
3-	-	-	4.3 Å2

Refinement step

Cycle: LAST / Resolution: 3.3→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	88296	0	552	0	88848

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	91424
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.354	1.962	124404
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.807	5	11096
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.248	24.273	4540
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.659	15	14124
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.953	15	480
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	12952
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	72312
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.622	1.5	55676
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.165	2	89760
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.995	3	35748
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.828	4.5	34644
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	B	3670	medium positional	0.28	0.5
2	C	3645	medium positional	0.26	0.5
3	D	3674	medium positional	0.23	0.5
4	E	3670	medium positional	0.26	0.5
5	F	3693	medium positional	0.28	0.5
6	G	3693	medium positional	0.21	0.5
7	H	3670	medium positional	0.28	0.5
8	I	3645	medium positional	0.24	0.5
9	J	3674	medium positional	0.24	0.5
10	K	3670	medium positional	0.25	0.5
11	L	3693	medium positional	0.23	0.5
12	M	3693	medium positional	0.22	0.5
13	N	3670	medium positional	0.25	0.5
14	O	3645	medium positional	0.24	0.5
15	P	3674	medium positional	0.24	0.5
16	Q	3670	medium positional	0.25	0.5
17	R	3693	medium positional	0.24	0.5
18	S	3693	medium positional	0.23	0.5
19	T	3670	medium positional	0.25	0.5
20	U	3645	medium positional	0.22	0.5
21	V	3674	medium positional	0.22	0.5
22	W	3670	medium positional	0.24	0.5
23	X	3693	medium positional	0.24	0.5
1	B	3670	medium thermal	0.92	2
2	C	3645	medium thermal	0.69	2
3	D	3674	medium thermal	1.09	2
4	E	3670	medium thermal	1	2
5	F	3693	medium thermal	0.75	2
6	G	3693	medium thermal	0.68	2
7	H	3670	medium thermal	0.7	2
8	I	3645	medium thermal	0.73	2
9	J	3674	medium thermal	1.03	2
10	K	3670	medium thermal	0.84	2
11	L	3693	medium thermal	0.72	2
12	M	3693	medium thermal	0.67	2
13	N	3670	medium thermal	0.71	2
14	O	3645	medium thermal	0.67	2
15	P	3674	medium thermal	0.69	2
16	Q	3670	medium thermal	0.89	2
17	R	3693	medium thermal	0.75	2
18	S	3693	medium thermal	0.7	2
19	T	3670	medium thermal	0.66	2
20	U	3645	medium thermal	0.7	2
21	V	3674	medium thermal	0.88	2
22	W	3670	medium thermal	0.7	2
23	X	3693	medium thermal	0.92	2