PDB-4zdi: Crystal structure of the M. tuberculosis CTP synthase PyrG (apo form)

ID or keywords:

Entry

Database: PDB / ID: 4zdi

Title

Crystal structure of the M. tuberculosis CTP synthase PyrG (apo form)

Components

CTP synthase

CTP synthetase

Keywords

LIGASE /

CTP synthase / PyrG / amidotransferase

Function / homology

Function and homology information

CTP synthase (glutamine hydrolysing) /

CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process /

glutaminase activity / CTP biosynthetic process / glutamine metabolic process /

ATP binding / identical protein binding /

metal ion binding ...
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.52 Å

Authors

Bellinzoni, M. / Barilone, N. / Alzari, P.M.

Funding support

France, 1items

Citation

Journal: Chem.Biol. / Year: 2015
Title: Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG.
Authors: Mori, G. / Chiarelli, L.R. / Esposito, M. / Makarov, V. / Bellinzoni, M. / Hartkoorn, R.C. / Degiacomi, G. / Boldrin, F. / Ekins, S. / de Jesus Lopes Ribeiro, A.L. / Marino, L.B. / ...

History

Deposition	Apr 17, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 1, 2015	Provider: repository / Type: Initial release
Revision 1.1	Aug 5, 2015	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4zdi.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb4zdi.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	4zdi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zd/4zdi ftp://data.pdbj.org/pub/pdb/validation_reports/zd/4zdi	HTTPS FTP

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Related structure data

Related structure data	4zdjSC 4zdkC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2ad5-2 6ns2-d 5o8l-d 3nva-d 2ad5-3 4uj4-1 3eut-d 5vbn-d 3zbn-d 4m26-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

4zdjSC

4zdkC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (4) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: CTP synthase

B: CTP synthase

C: CTP synthase

D: CTP synthase

E: CTP synthase

F: CTP synthase

G: CTP synthase

H: CTP synthase

hetero molecules

510 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: CTP synthase

hetero molecules

A: CTP synthase

hetero molecules

defined by author&software
128 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: CTP synthase

hetero molecules

B: CTP synthase

hetero molecules

defined by software
128 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: CTP synthase

D: CTP synthase

hetero molecules

defined by software
128 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

E: CTP synthase

H: CTP synthase

hetero molecules

defined by software
128 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

F: CTP synthase

G: CTP synthase

hetero molecules

defined by software
128 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	196.826, 196.826, 184.047
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	CTP synthase / CTP synthetase / CTP synthetase / UTP--ammonia ligase Mass: 63770.953 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: pyrG, Rv1699, MTCI125.21 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WHK7, CTP synthase (glutamine hydrolysing)
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca

#1: Protein

CTP synthase /

CTP synthetase / CTP synthetase / UTP--ammonia ligase

Mass: 63770.953 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: pyrG, Rv1699, MTCI125.21 / Plasmid: pET-28a / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WHK7, CTP synthase (glutamine hydrolysing)

#2: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.5 Å³/Da / Density % sol: 64.8 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG8000, 200 mM Ca acetate, 100 mM Hepes pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9801 Å / Relative weight: 1
Reflection	Resolution: 3.52→49.21 Å / Num. obs: 85758 / % possible obs: 98.4 % / Redundancy: 3.8 % / B_iso Wilson estimate: 69.88 Å² / R_merge(I) obs: 0.137 / Net I/σ(I): 8.6
Reflection shell	Resolution: 3.52→3.58 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.998 / Mean I/σ(I) obs: 1.3 / % possible all: 92.1

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Processing

Software

Name	Version	Classification
BUSTER	2.10.1	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4ZDJ

4zdj

Resolution: 3.52→49.21 Å / Cor.coef. F_o:F_c: 0.8712 / Cor.coef. F_o:F_c free: 0.8705 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R_free Blow DPI: 0.447

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2209	4288	5.01 %	RANDOM
R_work	0.2128	-	-	-
obs	0.2132	85620	98.62 %	-

Displacement parameters

B_iso mean: 111 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	28.0945 Å²	0 Å²	0 Å²
2-	-	28.0945 Å²	0 Å²
3-	-	-	-56.189 Å²

Refine analyze

Luzzati coordinate error obs: 0.81 Å

Refinement step

Cycle: 1 / Resolution: 3.52→49.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30929	0	8	0	30937

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.008	31615	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	0.89	43267	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		13921	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		638	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		4834	HARMONIC	5
X-RAY DIFFRACTION	t_it		31615	HARMONIC	20
X-RAY DIFFRACTION	t_nbd		0	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_omega_torsion	1.65
X-RAY DIFFRACTION	t_other_torsion	2.72
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		4321	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		35111	SEMIHARMONIC	4

LS refinement shell

Resolution: 3.52→3.61 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.2577	323	5.14 %
R_work	0.2516	5962	-
all	0.252	6285	-
obs	-	-	98.62 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.0878	-0.7453	0.474	1.2944	0.2108	2.1669	0.0226	-0.0293	0.1119	0.1014	0.0882	-0.0941	0.0127	0.0964	-0.1108	-0.0703	-0.0019	0.1002	0.0007	0.034	-0.1523	48.383	36.9348	-8.9464
2	0.2528	-0.6045	1.5685	0	0.4817	1.8476	0.0041	-0.0272	-0.0079	0.0628	0.0216	-0.0123	0.013	-0.014	-0.0257	0.0303	0.0461	-0.0732	0.0798	-0.0844	-0.0153	64.1252	30.7574	8.6993
3	4.5499	-1.3186	-1.0512	3.055	1.6759	1.7292	-0.0408	0.138	-0.0676	-0.0751	0.0152	-0.0357	-0.0365	-0.0803	0.0256	-0.109	0.0637	0.0213	0.0204	0.0601	-0.1889	73.385	12.5682	-15.2181
4	2.3756	-0.3942	-0.4973	2.4137	-0.4307	0.8717	0.0267	0.0317	0.1832	-0.2621	-0.0884	-0.1762	0.1353	0.0452	0.0617	0.0462	0.0935	0.0914	-0.055	-0.0086	-0.2055	46.5417	-32.4548	2.9061
5	0	0.0693	-2.8359	0.3656	-2.2551	1.7577	0	0.0368	0.0182	-0.0157	0.0042	-0.0065	0.0239	0.0124	-0.0041	0.0414	0.1163	0.1405	0.0725	0.0898	-0.0149	50.242	-17.2721	-15.1092
6	2.7449	-0.7495	0.1081	5.0341	0.1841	1.5977	0.0283	0.0267	0.0013	-0.0928	-0.2153	-0.0574	0.1612	-0.0299	0.187	0.012	0.0888	-0.0128	-0.0379	0.0376	-0.2967	22.6155	-7.0522	-2.806
7	2.995	0.3889	0.4354	1.9508	-0.0898	1.1233	-0.134	0.0728	0.1545	-0.1952	0.3083	-0.0515	-0.003	0.0592	-0.1743	0.0732	-0.1433	0.0309	0.0339	0.0727	-0.2964	49.295	15.5032	35.4329
8	0.1317	-0.0637	1.6337	0	-1.2868	1.7429	0.0002	0.0242	0.001	-0.0213	0.0074	0.0104	-0.0107	0.0261	-0.0077	0.1393	-0.1211	-0.0775	0.0388	0.1438	-0.0928	33.408	11.6692	17.8433
9	5.7278	1.8171	-0.664	2.9135	-0.955	1.1584	-0.1437	-0.0527	-0.1857	-0.0321	0.0435	-0.0034	-0.1764	0.039	0.1002	0.029	-0.0787	0.0054	-0.0426	0.0078	-0.2639	24.4023	-9.1736	40.3607
10	1.1899	-0.4301	0.4871	3.4896	-0.0773	1.4018	-0.0672	-0.1058	0.1127	-0.0132	0.1459	-0.2815	-0.0226	-0.0442	-0.0786	-0.1609	0.152	-0.0892	0.1278	-0.1264	-0.188	66.5946	24.4391	66.2805
11	0.37	0.5161	1.2261	0.6019	2.2931	0.7119	0.0029	-0.02	0.0121	0.0435	0.0072	-0.0188	-0.0293	-0.0135	-0.0101	0.0239	0.1051	-0.1134	0.0269	-0.1397	0.0619	83.4438	30.2088	83.0138
12	3.8502	-1.272	-0.1336	3.1175	0.1491	1.5549	-0.0677	0.0248	-0.0301	-0.046	-0.0279	-0.068	-0.052	-0.165	0.0956	-0.1661	0.152	-0.1155	0.1113	-0.0384	-0.2066	92.3569	1.2106	73.5752
13	1.2251	0.0984	-0.5609	3.2057	-0.44	2.0674	-0.0746	-0.1488	0.0587	0.0926	0.1829	0.2343	0.1042	-0.013	-0.1083	-0.1655	0.1511	-0.1119	0.0804	-0.0692	-0.1206	43.4994	52.5426	65.5275
14	0.1332	-0.1722	-1.0794	0.0357	-1.0032	1.0721	0.0019	-0.017	-0.005	0.0408	0.0032	0.01	0.0039	0.0166	-0.0051	0.0732	0.0785	0.048	0.0256	0.0772	-0.0039	28.0185	48.8314	83.8902
15	3.0819	-0.7816	0.2596	1.9347	-0.4177	1.3825	-0.0286	-0.026	-0.0168	-0.0582	-0.0013	0.087	-0.0303	-0.0024	0.0299	-0.2072	0.1407	-0.0391	-0.034	-0.1374	0.0984	18.0561	76.4072	71.5567
16	3.7244	-0.001	0.6501	1.5587	0.6704	1.9018	0.0622	0.1545	-0.158	-0.1309	-0.0702	-0.1403	-0.0349	-0.0432	0.008	-0.0676	0.1519	0.1461	-0.1337	-0.0052	-0.085	74.3767	-55.483	1.7916
17	0.4238	0.4485	1.3203	0.295	1.0436	1.7274	0.0018	0.0343	-0.0029	-0.0261	0.0053	-0.0017	-0.0219	-0.0112	-0.007	0.0327	0.1058	-0.0458	0.0551	-0.0965	0.0233	68.9356	-72.1675	-15.2071
18	2.5991	-2.5053	-0.2043	4.0424	0.1836	0.589	0.0427	0.0474	0.0384	0.0615	-0.1615	-0.1131	-0.0663	-0.0741	0.1189	-0.0707	0.1512	0.1469	-0.0807	0.0484	-0.0887	97.9416	-81.1464	-5.5571
19	1.6861	0.2009	-0.5214	1.6262	0.2197	2.3645	0.0282	-0.1141	0.0734	0.183	-0.0847	-0.1046	0.0118	0.0107	0.0565	0.0305	-0.0722	0.1294	-0.1937	-0.0598	-0.0277	82.0221	-38.2862	33.1303
20	0.0608	-0.3549	-1.1099	0.269	0.9668	1.7111	0.001	-0.037	-0.0053	0.0134	0.0128	0.0049	0.0269	-0.0185	-0.0138	0.0336	-0.0321	0.0388	0.0109	-0.0813	-0.0002	85.631	-22.0457	50.6417
21	2.2049	0.6409	-0.9324	3.6691	-1.3351	0.6255	0.008	-0.0221	-0.004	-0.061	-0.0658	-0.086	0.0691	-0.0528	0.0578	-0.0465	-0.1427	0.0068	-0.196	-0.0758	0.1153	106.79	-13.1408	28.807
22	1.6745	1.9609	-1.0008	1.7421	1.2808	2.8817	-0.1459	-0.0272	0.0565	-0.3089	0.3711	-0.0797	-0.1097	-0.1157	-0.2252	0.1003	-0.152	-0.1483	-0.0741	-0.0234	-0.2678	58.5339	62.0513	31.2089
23	0.0166	0.6321	-0.7009	0	-0.512	1.4028	0.0024	0.0266	0.0091	-0.0243	0.0095	-0.0188	-0.0228	-0.0208	-0.012	0.0663	-0.1409	0.0166	0.0236	-0.0797	-0.0663	73.6073	67.5029	13.1746
24	4.3332	1.8331	0.5354	2.0763	0.7563	0.9979	-0.1137	-0.1448	0.1151	-0.196	0.1481	-0.0506	0.0419	-0.1068	-0.0344	0.0822	-0.152	-0.0292	-0.1363	-0.1382	-0.1946	84.3555	85.713	37.245

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|7 - A\|278 }
2	X-RAY DIFFRACTION	2	{ A\|279 - A\|298 }
3	X-RAY DIFFRACTION	3	{ A\|299 - A\|551 }
4	X-RAY DIFFRACTION	4	{ B\|7 - B\|278 }
5	X-RAY DIFFRACTION	5	{ B\|279 - B\|298 }
6	X-RAY DIFFRACTION	6	{ B\|299 - B\|551 }
7	X-RAY DIFFRACTION	7	{ C\|7 - C\|278 }
8	X-RAY DIFFRACTION	8	{ C\|279 - C\|298 }
9	X-RAY DIFFRACTION	9	{ C\|299 - C\|551 }
10	X-RAY DIFFRACTION	10	{ D\|7 - D\|278 }
11	X-RAY DIFFRACTION	11	{ D\|279 - D\|298 }
12	X-RAY DIFFRACTION	12	{ D\|299 - D\|551 }
13	X-RAY DIFFRACTION	13	{ E\|7 - E\|278 }
14	X-RAY DIFFRACTION	14	{ E\|279 - E\|298 }
15	X-RAY DIFFRACTION	15	{ E\|299 - E\|551 }
16	X-RAY DIFFRACTION	16	{ F\|6 - F\|278 }
17	X-RAY DIFFRACTION	17	{ F\|279 - F\|298 }
18	X-RAY DIFFRACTION	18	{ F\|299 - F\|551 }
19	X-RAY DIFFRACTION	19	{ G\|7 - G\|278 }
20	X-RAY DIFFRACTION	20	{ G\|279 - G\|298 }
21	X-RAY DIFFRACTION	21	{ G\|299 - G\|551 }
22	X-RAY DIFFRACTION	22	{ H\|7 - H\|278 }
23	X-RAY DIFFRACTION	23	{ H\|279 - H\|298 }
24	X-RAY DIFFRACTION	24	{ H\|299 - H\|551 }

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Yorodumi