PDB-4acf: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS GLUTAMINE SYNTHET...

ID or keywords:

Entry

Database: PDB / ID: 4acf

Title

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS GLUTAMINE SYNTHETASE IN COMPLEX WITH IMIDAZOPYRIDINE INHIBITOR ((4-(6-BROMO-3-(BUTYLAMINO)IMIDAZO(1,2-A)PYRIDIN-2-YL)PHENOXY) ACETIC ACID) AND L-METHIONINE-S-SULFOXIMINE PHOSPHATE.

Components

GLUTAMINE SYNTHETASE 1

Keywords

LIGASE / NUCLEOTIDE-BINDING / SYNTHETASE / TRI-SUBSTITUTED IMIDAZOLE / TAUT STATE / RV2220 / MT2278 / GLNA1

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 ...
Similarity search - Function

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2 Å

Authors

Nilsson, M.T. / Mowbray, S.L.

Citation

Journal: Medchemcomm / Year: 2012
Title: Synthesis, Biological Evaluation and X-Ray Crystallographic Studies of Imidazo(1,2-A)Pyridine-Based Mycobacterium Tuberculosis Glutamine Synthetase Inhibitors
Authors: Nordqvist, A. / Nilsson, M.T. / Lagerlund, O. / Muthas, D. / Gising, J. / Yahiaoui, S. / Odell, L.R. / Srinivasa, B.R. / Larhed, M. / Mowbray, S.L. / Karlen, A.

History

Deposition	Dec 15, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 24, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2019	Group: 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 1.2	May 15, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.3	Dec 20, 2023	Group: 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 / 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_database_status.status_code_sf / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4acf.cif.gz	605.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4acf_validation.pdf.gz	3.1 MB	Display	wwPDB validaton report
Full document	4acf_full_validation.pdf.gz	3.2 MB	Display
Data in XML	4acf_validation.xml.gz	116.2 KB	Display
Data in CIF	4acf_validation.cif.gz	169.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ac/4acf ftp://data.pdbj.org/pub/pdb/validation_reports/ac/4acf	HTTPS FTP

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Related structure data

Related structure data	2bvcS 1hto 1htq 2wgs 2whi 3zxr 3zxv S: Starting model for refinement
Similar structure data	2whi-1 3zxr-1 2bvc-1 1f52-d 1htq-2 1hto-1 1fpy-d 3zxv-1 1hto-2 1htq-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#30 - Jun 2002 Glutamine Synthetase similarity (15)

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

hetero molecules

333 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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

hetero molecules

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

defined by author&software
666 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	132.590, 227.390, 202.350
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	5 - 402
2	1	1	4	B	5 - 402
3	1	1	4	C	5 - 402
4	1	1	4	D	5 - 402
5	1	1	4	E	5 - 402
6	1	1	4	F	5 - 402
1	1	2	4	A	416 - 478
2	1	2	4	B	416 - 478
3	1	2	4	C	416 - 478
4	1	2	4	D	416 - 478
5	1	2	4	E	416 - 478
6	1	2	4	F	416 - 478
1	1	3	1	A	501 - 921
2	1	3	1	B	501 - 921
3	1	3	1	C	501 - 921
4	1	3	1	D	501 - 921
5	1	3	1	E	501 - 921
6	1	3	1	F	501 - 921

NCS ensembles :

ID
1
2
3

NCS oper:

ID	Code	Matrix
1	given	(0.517068, 0.850975, -0.092099), (-0.850731, 0.499078, -0.164856), (-0.094324, 0.163593, 0.982008)
2	given	(-0.442225, 0.850522, -0.284692), (-0.849523, -0.499006, -0.171183), (-0.287658, 0.166151, 0.943211)
3	given	(-0.92279, 0.000635, -0.385303), (-0.002084, -0.999992, 0.003341), (-0.385298, 0.003886, 0.922784)
4	given	(-0.444996, -0.848616, -0.286058), (0.846078, -0.503078, 0.176253), (-0.29348, -0.163595, 0.941863)
5	given	(0.516762, -0.850726, -0.096035), (0.850189, 0.496747, 0.174416), (-0.100675, -0.17178, 0.979978)

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	GLUTAMINE SYNTHETASE 1 / GLUTAMATE--AMMONIA LIGASE 1 Mass: 54584.730 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-478 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCR T7/CT-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GJ4745 References: UniProt: P0A590, UniProt: P9WN39*PLUS, glutamine synthetase

#1: Protein

GLUTAMINE SYNTHETASE 1 / GLUTAMATE--AMMONIA LIGASE 1

Mass: 54584.730 Da / Num. of mol.: 6 / Fragment: RESIDUES 2-478
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCR T7/CT-TOPO / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): GJ4745
References: UniProt: P0A590, UniProt: P9WN39*PLUS, glutamine synthetase

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Non-polymers , 6 types, 1974 molecules

#2: Chemical	ChemComp-46B / {4-[6-BROMO-3-(BUTYLAMINO)IMIDAZO[1,2-A]PYRIDIN-2-YL]PHENOXY}ACETIC ACID Mass: 418.284 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₉H₂₀BrN₃O₃
#3: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-P3S / L-METHIONINE-S-SULFOXIMINE PHOSPHATE Mass: 260.205 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₅H₁₃N₂O₆PS
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO₄
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1926 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	PROTEIN 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. E. COLI STRAIN GJ4745 IS ADENYLYLTRANSFERASE DEFICIENT ( GLNE-)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.2 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M TRIS-HCL, PH 7.5, 0.2 M MAGNESIUM CHLORIDE, 39% (V/V) PEG 400) AND PROTEIN SOLUTION (13 G/L IN 0.1 M TRIS-HCL, PH 7.5, 0.125 M SODIUM CHLORIDE, 0.004 M ...Details: EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M TRIS-HCL, PH 7.5, 0.2 M MAGNESIUM CHLORIDE, 39% (V/V) PEG 400) AND PROTEIN SOLUTION (13 G/L IN 0.1 M TRIS-HCL, PH 7.5, 0.125 M SODIUM CHLORIDE, 0.004 M MAGNESIUM CHLORIDE, 4%(V/V) DMSO, 0.001 M INHIBITOR, 0.004 M MSOP), HANGING-DROP, VAPOR DIFFUSION, TEMPERATURE 294K.

Crystal

Density Matthews: 2.33 Å³/Da / Density % sol: 47.2 %

Crystal grow

Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M TRIS-HCL, PH 7.5, 0.2 M MAGNESIUM CHLORIDE, 39% (V/V) PEG 400) AND PROTEIN SOLUTION (13 G/L IN 0.1 M TRIS-HCL, PH 7.5, 0.125 M SODIUM CHLORIDE, 0.004 M ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0683
Detector	Type: ADSC CCD / Detector: CCD / Date: Sep 8, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0683 Å / Relative weight: 1
Reflection	Resolution: 2→20 Å / Num. obs: 192509 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / R_merge(I) obs: 0.08 / Net I/σ(I): 15.5
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 4.7 / % possible all: 96.4

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: PDB ENTRY 2BVC

2bvc

Resolution: 2→20 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.941 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 403-415 ARE EXCLUDED FROM THE NCS DUE TO DIFFERENCES AS A RESULT OF CRYSTAL CONTACTS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19771	10190	5 %	RANDOM
R_work	0.16533	-	-	-
obs	0.16695	192509	99.14 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 17.118 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	0 Å²
2-	-	-1.32 Å²	0 Å²
3-	-	-	1.33 Å²

Refinement step

Cycle: LAST / Resolution: 2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22572	0	306	1926	24804

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	23484
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	15828
X-RAY DIFFRACTION	r_angle_refined_deg	1.43	1.966	31944
X-RAY DIFFRACTION	r_angle_other_deg	4.118	3	38442
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.277	5	2844
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.756	24.197	1158
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.94	15	3624
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.054	15	126
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	3318
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	26478
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	4908
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	0.667	1.5	14268
X-RAY DIFFRACTION	r_mcbond_other	0	1.5	5712
X-RAY DIFFRACTION	r_mcangle_it	1.195	2	23004
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.963	3	9216
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.077	4.5	8940
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

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
3	1	A	393	tight positional	0.07	0.05
3	2	B	393	tight positional	0.07	0.05
3	3	C	393	tight positional	0.06	0.05
3	4	D	393	tight positional	0.07	0.05
3	5	E	393	tight positional	0.08	0.05
3	6	F	393	tight positional	0.07	0.05
1	1	A	5302	medium positional	0.13	0.5
1	2	B	5302	medium positional	0.12	0.5
1	3	C	5302	medium positional	0.12	0.5
1	4	D	5302	medium positional	0.13	0.5
1	5	E	5302	medium positional	0.15	0.5
1	6	F	5302	medium positional	0.12	0.5
2	1	A	885	medium positional	0.13	0.5
2	2	B	885	medium positional	0.16	0.5
2	3	C	885	medium positional	0.11	0.5
2	4	D	885	medium positional	0.12	0.5
2	5	E	885	medium positional	0.12	0.5
2	6	F	885	medium positional	0.12	0.5
3	1	A	393	tight thermal	0.26	0.5
3	2	B	393	tight thermal	0.26	0.5
3	3	C	393	tight thermal	0.31	0.5
3	4	D	393	tight thermal	0.2	0.5
3	5	E	393	tight thermal	0.31	0.5
3	6	F	393	tight thermal	0.32	0.5
1	1	A	5302	medium thermal	0.94	2
1	2	B	5302	medium thermal	1.04	2
1	3	C	5302	medium thermal	1.31	2
1	4	D	5302	medium thermal	0.74	2
1	5	E	5302	medium thermal	1.33	2
1	6	F	5302	medium thermal	1.19	2
2	1	A	885	medium thermal	0.77	2
2	2	B	885	medium thermal	0.75	2
2	3	C	885	medium thermal	1.23	2
2	4	D	885	medium thermal	0.64	2
2	5	E	885	medium thermal	1.15	2
2	6	F	885	medium thermal	0.93	2

LS refinement shell

Resolution: 2→2.051 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.274	687	-
R_work	0.226	13294	-
obs	-	-	93.79 %

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