PDB-3tqi: Structure of the GMP synthase (guaA) from Coxiella burnetii

ID or keywords:

Entry

Database: PDB / ID: 3tqi

Title

Structure of the GMP synthase (guaA) from Coxiella burnetii

Components

GMP synthase [glutamine-hydrolyzing]

Keywords

LIGASE / GMP synthase

Function / homology

Function and homology information

GMP synthase activity / GMP synthase (glutamine-hydrolysing) / GMP biosynthetic process / glutamine metabolic process / ATP binding / cytosol
Similarity search - Function

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.84 Å

Authors

Franklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.

Citation

Journal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.

History

Deposition	Sep 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Jan 20, 2016	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3tqi.cif.gz	732.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3tqi.ent.gz	614.3 KB	Display	PDB format
PDBx/mmJSON format	3tqi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3tqi_validation.pdf.gz	468.8 KB	Display	wwPDB validaton report
Full document	3tqi_full_validation.pdf.gz	513.7 KB	Display
Data in XML	3tqi_validation.xml.gz	64.3 KB	Display
Data in CIF	3tqi_validation.cif.gz	86.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tq/3tqi ftp://data.pdbj.org/pub/pdb/validation_reports/tq/3tqi	HTTPS FTP

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Related structure data

Related structure data	3tq8C 3tq9C 3tqaC 3tqbC 3tqcC 3tqdC 3tqeC 3tqfC 3tqgC 3tqhC 3tqjC 3tqlC 3tqmC 3tqnC 3tqoC 3tqpC 3tqqC 3tqrC 3tqsC 3tqtC 3tquC 3tqwC 3tqxC 3tqyC 3tqzC 3tr0C 3tr1C 3tr2C 3tr3C 3tr4C 3tr5C 3tr6C 3tr7C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trfC 3trgC 3trhC 3triC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4nbqC 4ng4C C: citing same article (ref.)
Similar structure data	5tw7-1 5tw7-3 5tw7-2 2ywc-2 2ywb-2 2ywb-1 6qgc-d 3mcg-1 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

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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: GMP synthase [glutamine-hydrolyzing]

B: GMP synthase [glutamine-hydrolyzing]

C: GMP synthase [glutamine-hydrolyzing]

D: GMP synthase [glutamine-hydrolyzing]

236 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GMP synthase [glutamine-hydrolyzing]

B: GMP synthase [glutamine-hydrolyzing]

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

2

C: GMP synthase [glutamine-hydrolyzing]

D: GMP synthase [glutamine-hydrolyzing]

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	74.913, 143.953, 107.885
Angle α, β, γ (deg.)	90.00, 97.66, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
1	2	A
2	2	B
3	2	C
4	2	D
1	3	A
2	3	B
3	3	C
4	3	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	1 - 208
2	1	1	4	B	1 - 208
3	1	1	4	C	1 - 208
4	1	1	4	D	1 - 208
1	1	2	4	A	209 - 416
2	1	2	4	B	209 - 416
3	1	2	4	C	209 - 416
4	1	2	4	D	209 - 416
1	1	3	4	A	417 - 523
2	1	3	4	B	417 - 523
3	1	3	4	C	417 - 523
4	1	3	4	D	417 - 523

NCS ensembles :

ID
1
2
3

Details

The biological unit of this protein is a dimer, of which there are two in the asymmetric unit: chains A+B, and chains C+D

#1: Protein	GMP synthase [glutamine-hydrolyzing] / GMP synthetase / Glutamine amidotransferase Mass: 59034.160 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 Nine Mile Phase I / Gene: CBU_1341, guaA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q83BZ6, GMP synthase (glutamine-hydrolysing)

#1: Protein

GMP synthase [glutamine-hydrolyzing] / GMP synthetase / Glutamine amidotransferase

Mass: 59034.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Coxiella burnetii (bacteria) / Strain: RSA 493 Nine Mile Phase I / Gene: CBU_1341, guaA / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83BZ6, GMP synthase (glutamine-hydrolysing)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.62 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M imidazole, 0.1 M calcium acetate, 19% PEG 1000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2011
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.84→100 Å / Num. all: 53394 / Num. obs: 53026 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / R_sym value: 0.073 / Net I/σ(I): 20.3
Reflection shell	Resolution: 2.85→2.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.3 / R_sym value: 0.447 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
SOLVE		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.84→39.01 Å / Cor.coef. F_o:F_c: 0.908 / Cor.coef. F_o:F_c free: 0.879 / SU B: 42.94 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R Free: 0.441
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28133	2691	5.1 %	RANDOM
R_work	0.24484	-	-	-
obs	0.24666	50308	98.68 %	-
all	-	53708	-	-

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: 48.524 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.24 Å²	0 Å²	1.76 Å²
2-	-	0.28 Å²	0 Å²
3-	-	-	-1.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.84→39.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14708	0	0	0	14708

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	15032
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	10300
X-RAY DIFFRACTION	r_angle_refined_deg	1.221	1.963	20340
X-RAY DIFFRACTION	r_angle_other_deg	0.839	3	25160
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.403	5	1832
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.202	24.244	688
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.875	15	2624
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.496	15	84
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	2276
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	16484
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2956
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	0.203	1.5	9220
X-RAY DIFFRACTION	r_mcbond_other	0.041	1.5	3744
X-RAY DIFFRACTION	r_mcangle_it	0.423	2	14920
X-RAY DIFFRACTION	r_scbond_it	0.762	3	5812
X-RAY DIFFRACTION	r_scangle_it	1.322	4.5	5420
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
1	1	A	2534	medium positional	0.33	0.5
1	1	B	2534	medium positional	0.35	0.5
1	1	C	2534	medium positional	0.36	0.5
1	1	D	2534	medium positional	0.34	0.5
2	2	A	2430	medium positional	0.39	0.5
2	2	B	2430	medium positional	0.36	0.5
2	2	C	2430	medium positional	0.41	0.5
2	2	D	2430	medium positional	0.38	0.5
3	3	A	1288	medium positional	0.34	0.5
3	3	B	1288	medium positional	0.38	0.5
3	3	C	1288	medium positional	0.33	0.5
3	3	D	1288	medium positional	0.35	0.5
1	1	A	2534	medium thermal	0.14	2
1	1	B	2534	medium thermal	0.16	2
1	1	C	2534	medium thermal	0.14	2
1	1	D	2534	medium thermal	0.16	2
2	2	A	2430	medium thermal	0.15	2
2	2	B	2430	medium thermal	0.15	2
2	2	C	2430	medium thermal	0.14	2
2	2	D	2430	medium thermal	0.14	2
3	3	A	1288	medium thermal	0.12	2
3	3	B	1288	medium thermal	0.12	2
3	3	C	1288	medium thermal	0.12	2
3	3	D	1288	medium thermal	0.13	2

LS refinement shell

Resolution: 2.836→2.909 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.406	171	-
R_work	0.325	3411	-
obs	-	-	90.59 %

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	3.6434	-0.6346	-0.4264	6.7879	0.7709	2.0335	-0.0087	-0.1232	-0.2393	-0.0825	-0.1149	-0.7797	0.0707	0.332	0.1236	0.0815	0.0364	0.0014	0.3139	0.1472	0.1978	24.0024	47.1582	108.2457
2	1.812	0.4259	-1.318	3.6696	-1.2365	4.5123	0.1596	-0.0741	0.3479	-0.0063	-0.0665	-0.1289	-0.295	0.2244	-0.0931	0.2455	-0.064	0.0492	0.179	-0.0702	0.2525	17.0346	81.9948	98.8459
3	7.5679	0.3558	-3.417	5.874	-1.136	10.2964	0.0168	0.4686	0.0501	0.0001	-0.2895	0.3355	0.1197	-1.0258	0.2727	0.3678	-0.0446	0.1415	0.2579	-0.1402	0.1341	13.7408	72.1943	74.6411
4	8.5715	-0.3754	-1.5106	4.1042	-0.3437	2.6676	0.1871	0.2758	0.8363	-0.2708	-0.0127	0.1569	-0.1571	0.0559	-0.1743	0.1417	0.0308	-0.1086	0.1654	0.0524	0.2372	-5.7452	68.782	34.7943
5	3.0906	0.5683	0.4207	2.3989	1.3004	4.8333	0.0514	-0.068	0.2817	0.2317	-0.022	0.1208	-0.2618	0.169	-0.0293	0.167	-0.0095	0.0366	0.1856	0.0599	0.1508	30.1607	62.4201	39.4886
6	7.7497	1.7884	0.7266	6.3619	3.0911	8.8048	-0.0336	-0.0059	-0.2403	0.2992	-0.208	0.0278	0.8296	-0.2788	0.2416	0.4445	-0.0175	0.2053	0.1899	-0.0653	0.1248	23.5292	61.5103	64.8742
7	5.3349	0.7111	-0.8461	8.4242	-2.3753	3.0266	0.0798	-0.078	0.4011	0.0585	0.2197	0.7717	-0.0324	-0.3073	-0.2995	0.1219	0.0548	0.0304	0.1599	0.0089	0.2832	-16.7921	66.9966	105.1158
8	2.2596	0.3583	0.7863	2.6967	-0.1629	5.4075	-0.0693	0.1625	-0.0222	-0.216	0.0052	0.0983	0.4996	-0.398	0.0641	0.2777	-0.0478	0.046	0.2218	0.0262	0.1149	-9.7794	31.0574	105.2486
9	5.4799	1.5389	2.2536	7.5822	2.5686	9.1956	0.1654	0.2777	-0.1559	0.0466	-0.1403	-0.0548	-0.1022	0.704	-0.0251	0.3633	0.0124	-0.0701	0.2991	0.0687	0.0423	-5.6396	34.4992	79.6429
10	6.8171	-0.4678	1.4329	3.1245	-0.3979	2.4804	-0.0679	-0.1003	-0.7189	0.0404	-0.1121	-0.1344	0.2391	0.0078	0.1799	0.1666	0.032	0.1064	0.1118	0.0424	0.163	14.8067	28.007	38.8044
11	3.822	0.4179	-0.627	2.8134	-0.3814	3.9293	0.0232	-0.0161	-0.289	0.277	-0.1176	0.1521	0.3045	-0.2916	0.0944	0.2133	-0.032	-0.0686	0.1953	-0.0658	0.1571	-21.1071	35.3338	42.5403
12	6.8264	1.4935	-1.0105	4.8946	-2.0808	9.8686	-0.1615	0.0886	0.1484	0.1944	-0.0667	0.2398	-0.7853	0.189	0.2282	0.5042	-0.0269	-0.1402	0.2453	0.0453	0.0651	-14.9396	42.3707	67.1818

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 208
2	X-RAY DIFFRACTION	2	A	209 - 416
3	X-RAY DIFFRACTION	3	A	417 - 523
4	X-RAY DIFFRACTION	4	B	5 - 208
5	X-RAY DIFFRACTION	5	B	209 - 416
6	X-RAY DIFFRACTION	6	B	417 - 523
7	X-RAY DIFFRACTION	7	C	5 - 208
8	X-RAY DIFFRACTION	8	C	209 - 416
9	X-RAY DIFFRACTION	9	C	417 - 523
10	X-RAY DIFFRACTION	10	D	5 - 208
11	X-RAY DIFFRACTION	11	D	209 - 416
12	X-RAY DIFFRACTION	12	D	417 - 523

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