PDB-5tw7: Crystal structure of a GMP synthase (glutamine-hydrolyzing) from ...

ID or keywords:

Entry

Database: PDB / ID: 5tw7

Title

Crystal structure of a GMP synthase (glutamine-hydrolyzing) from Neisseria gonorrhoeae

Components

GMP synthase [glutamine-hydrolyzing]

Keywords

LIGASE / Neisseria gonorrhoeae / GMP / glutamine / structural genomics / NIAID / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

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

Biological species

Neisseria gonorrhoeae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.35 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of a GMP synthase (glutamine-hydrolyzing) from Neisseria gonorrhoeae
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D. / Fairman, J.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	Nov 11, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5tw7.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb5tw7.ent.gz	941.8 KB	Display	PDB format
PDBx/mmJSON format	5tw7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5tw7_validation.pdf.gz	465.8 KB	Display	wwPDB validaton report
Full document	5tw7_full_validation.pdf.gz	476.9 KB	Display
Data in XML	5tw7_validation.xml.gz	93.4 KB	Display
Data in CIF	5tw7_validation.cif.gz	131.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tw/5tw7 ftp://data.pdbj.org/pub/pdb/validation_reports/tw/5tw7	HTTPS FTP

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Related structure data

Related structure data	1gpmS S: Starting model for refinement
Similar structure data	3tqi-1 2ywb-2 2ywc-2 3tqi-2 2ywb-1 3ept-d 1b3q-d 3dor-2 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
Other databases	TargetTrack: NegoA.17876.a

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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]

E: GMP synthase [glutamine-hydrolyzing]

F: GMP synthase [glutamine-hydrolyzing]

hetero molecules

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

1

A: 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)

2

B: GMP synthase [glutamine-hydrolyzing]

E: GMP synthase [glutamine-hydrolyzing]

hetero molecules

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

3

C: GMP synthase [glutamine-hydrolyzing]

F: GMP synthase [glutamine-hydrolyzing]

hetero molecules

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

Unit cell

Length a, b, c (Å)	108.390, 109.350, 109.910
Angle α, β, γ (deg.)	115.33, 100.00, 108.06
Int Tables number	1
Space group name H-M	P1

#1: Protein	GMP synthase [glutamine-hydrolyzing] / GMP synthetase / Glutamine amidotransferase Mass: 58757.113 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: guaA, NGK_2643 / Production host: Escherichia coli (E. coli) References: UniProt: B4RJH7, GMP synthase (glutamine-hydrolysing)
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.51 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: NegoA.17876.a.B1.PW39722 at 25.5 mg/mL against MCSG1 screen condition C6: 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, 30% PEG400

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 20, 2016

Radiation

Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.35→46.116 Å / Num. obs: 166001 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 34.37 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.075 / R_rim(I) all: 0.087 / Χ²: 0.998 / Net I/σ(I): 14.95 / Num. measured all: 644834

Reflection shell

Diffraction-ID: 1

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	% possible all
2.35-2.41	0.517	2.88	48499	12497	12193	0.803	97.6
2.41-2.48	0.441	3.39				0.842	97.7
2.48-2.55	0.369	4.04				0.896	97.8
2.55-2.63	0.309	4.85				0.923	97.9
2.63-2.71	0.252	5.95				0.943	97.8
2.71-2.81	0.208	7.13				0.957	98.2
2.81-2.91	0.17	8.53				0.971	98.2
2.91-3.03	0.131	10.84				0.982	98.2
3.03-3.17	0.104	13.24				0.988	98.3
3.17-3.32	0.079	16.48				0.993	98.4
3.32-3.5	0.063	19.91				0.995	98.2
3.5-3.72	0.053	22.93				0.996	98.4
3.72-3.97	0.044	26.4				0.997	98.4
3.97-4.29	0.038	29.79				0.997	98.2
4.29-4.7	0.034	32.33				0.998	98
4.7-5.25	0.034	32.8				0.997	98.3
5.25-6.07	0.036	31.05				0.998	98.3
6.07-7.43	0.033	32.97				0.998	98.7
7.43-10.51	0.026	39.45				0.998	97.9
10.51-46.116	0.026	41.02				0.998	95.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XSCALE		data scaling
MOLREP		phasing
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1GPM

1gpm

Resolution: 2.35→46.116 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 23.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2232	7928	4.78 %
R_work	0.1858	-	-
obs	0.1875	165962	98.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.35→46.116 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22619	0	2	336	22957

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	23182
X-RAY DIFFRACTION	f_angle_d	0.894	31504
X-RAY DIFFRACTION	f_dihedral_angle_d	15.562	13774
X-RAY DIFFRACTION	f_chiral_restr	0.056	3545
X-RAY DIFFRACTION	f_plane_restr	0.006	4123

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.35-2.3767	0.313	284	0.2493	5202	X-RAY DIFFRACTION	97
2.3767-2.4046	0.2959	255	0.2408	5233	X-RAY DIFFRACTION	98
2.4046-2.434	0.2763	253	0.2333	5248	X-RAY DIFFRACTION	98
2.434-2.4648	0.2768	273	0.2308	5279	X-RAY DIFFRACTION	98
2.4648-2.4972	0.2748	284	0.225	5240	X-RAY DIFFRACTION	98
2.4972-2.5314	0.2629	266	0.2192	5202	X-RAY DIFFRACTION	98
2.5314-2.5676	0.2954	276	0.2287	5231	X-RAY DIFFRACTION	98
2.5676-2.6059	0.2988	281	0.2251	5248	X-RAY DIFFRACTION	98
2.6059-2.6466	0.2662	276	0.2234	5254	X-RAY DIFFRACTION	98
2.6466-2.69	0.2681	238	0.2197	5259	X-RAY DIFFRACTION	98
2.69-2.7364	0.2643	272	0.2193	5261	X-RAY DIFFRACTION	98
2.7364-2.7861	0.2738	248	0.2266	5292	X-RAY DIFFRACTION	98
2.7861-2.8397	0.3189	253	0.2276	5289	X-RAY DIFFRACTION	98
2.8397-2.8977	0.2606	283	0.2264	5232	X-RAY DIFFRACTION	98
2.8977-2.9607	0.2617	248	0.2225	5317	X-RAY DIFFRACTION	98
2.9607-3.0295	0.2622	264	0.2178	5267	X-RAY DIFFRACTION	99
3.0295-3.1053	0.302	251	0.2269	5283	X-RAY DIFFRACTION	98
3.1053-3.1892	0.2563	280	0.221	5275	X-RAY DIFFRACTION	98
3.1892-3.283	0.2401	270	0.2171	5283	X-RAY DIFFRACTION	99
3.283-3.3889	0.247	286	0.1995	5238	X-RAY DIFFRACTION	99
3.3889-3.51	0.243	262	0.1905	5309	X-RAY DIFFRACTION	99
3.51-3.6505	0.2133	258	0.179	5307	X-RAY DIFFRACTION	99
3.6505-3.8166	0.2008	258	0.1689	5274	X-RAY DIFFRACTION	99
3.8166-4.0177	0.197	251	0.1562	5312	X-RAY DIFFRACTION	99
4.0177-4.2692	0.1793	215	0.1479	5300	X-RAY DIFFRACTION	98
4.2692-4.5986	0.1664	275	0.1331	5262	X-RAY DIFFRACTION	98
4.5986-5.0609	0.1503	266	0.1354	5285	X-RAY DIFFRACTION	99
5.0609-5.792	0.192	283	0.1584	5302	X-RAY DIFFRACTION	99
5.792-7.2926	0.1975	241	0.1669	5330	X-RAY DIFFRACTION	99
7.2926-46.1246	0.1584	278	0.156	5220	X-RAY DIFFRACTION	98

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	3.8398	0.3474	-0.2058	2.3337	-0.3881	1.5777	-0.003	-0.0491	-0.0916	-0.0927	-0.0051	0.0138	-0.0216	0.0596	0.0282	0.2077	-0.0604	0.0128	0.4376	-0.0679	0.2412	-75.8287	12.3429	58.0307
2	2.716	-0.4721	-0.2154	2.8809	-1.3688	2.8432	-0.1016	-0.291	0.2308	0.3094	-0.121	-0.2912	-0.1942	0.399	0.1822	0.2302	-0.0366	-0.0512	0.3059	-0.0283	0.2907	-63.5133	-21.8572	20.9554
3	0.612	0.568	-0.4662	1.4388	0.0377	0.5731	-0.0768	0.4148	0.9316	0.086	0.3268	0.5588	-0.1157	-0.2082	-0.2023	0.3293	0.0742	-0.0709	0.4414	0.1908	0.8632	-62.7881	8.9589	-0.4866
4	3.2465	-0.0786	0.5171	2.2995	-0.0164	3.4175	0.0043	0.3169	0.1202	-0.0463	0.0454	0.205	-0.1397	-0.143	-0.0456	0.1702	0.0001	-0.0346	0.2541	0.0247	0.4734	-37.1877	5.5135	1.4155
5	3.2192	1.1754	1.3339	3.9665	-0.0778	4.2574	-0.1734	-0.2407	-0.6718	0.1155	0.0896	0.0427	0.4019	-0.0944	0.0583	0.2804	0.0497	0.1304	0.3302	0.0365	0.4794	-101.0691	43.3422	5.9307
6	1.8624	0.077	0.1548	0.7309	0.3948	4.7147	-0.2138	-0.0344	-0.5006	-0.0939	0.0054	0.0279	0.1994	0.1287	0.2324	0.2646	-0.0082	0.0839	0.324	-0.0009	0.4403	-94.3385	49.3926	0.9553
7	1.3689	-0.3716	0.559	0.6855	0.0093	1.163	-0.1317	-0.9162	-0.2895	0.171	0.1762	0.0922	0.0928	-0.5313	0.0101	0.4081	0.0692	0.1135	0.8055	0.2164	0.448	-89.4849	49.0656	36.3379
8	4.235	-0.374	-0.1019	2.283	0.5337	2.9182	0.0323	-0.278	0.272	0.1686	0.1219	0.1603	-0.0444	-0.2891	-0.1381	0.2141	0.0398	0.0444	0.3366	0.0932	0.3476	-66.5037	51.9815	28.7899
9	2.1615	-0.1208	0.0271	3.9671	1.12	1.8189	0.0365	0.6216	0.1934	-0.3873	-0.134	-0.0002	-0.1465	-0.0842	0.074	0.2659	-0.0166	-0.013	0.5297	0.0358	0.2461	-117.9517	27.7279	71.9553
10	0.4529	0.4646	0.4591	1.0126	0.7971	1.292	-0.056	0.6548	-0.5035	0.0705	-0.2047	0.3942	0.0794	-0.5613	0.3736	0.3542	-0.4241	0.1257	1.0095	-0.6833	0.7733	-123.5878	-5.7048	62.8617
11	0.8683	0.0571	-0.7571	0.8348	0.6063	2.3397	-0.3141	0.5043	-0.597	-0.014	-0.3164	0.2283	0.1414	-0.6765	0.3148	0.4	-0.1626	0.0918	0.6826	-0.3554	0.4778	-110.1196	-6.0669	55.1017
12	2.9338	0.736	0.2807	2.9887	0.285	2.8417	-0.055	0.0019	-0.2644	0.0122	-0.1159	-0.0237	0.1279	-0.1313	0.1453	0.2017	-0.0805	0.0294	0.4245	-0.0493	0.2964	-87.6184	1.6306	59.3408
13	0.8855	0.1255	0.1235	1.2239	1.5141	3.4153	-0.1295	0.1717	0.345	-0.1704	-0.052	0.0549	-0.2448	-0.0027	0.1444	0.2522	0.0212	-0.05	0.2343	0.0669	0.3228	6.235	-6.5747	-12.7358
14	2.0363	-1.4961	-0.8026	1.6168	0.2484	0.8055	0.0396	-0.1945	0.3204	0.0244	0.1585	-0.1372	-0.0688	0.1374	-0.1734	0.2936	-0.0138	-0.0548	0.1803	-0.065	0.3977	-0.2546	10.2031	16.7804
15	1.6632	0.1166	0.4178	2.1775	0.7234	2.7461	0.0713	-0.0482	-0.3153	0.1437	0.011	0.0503	0.0137	-0.0472	-0.0914	0.1916	0.0151	-0.0162	0.1695	0.0386	0.4488	-23.5726	3.5464	12.2398
16	2.2153	-0.2887	0.1246	3.2302	0.8366	1.9652	-0.0543	-0.1581	0.0721	0.1214	-0.0392	0.2112	0.0873	-0.0358	0.097	0.2301	-0.0026	0.0157	0.1142	-0.0118	0.206	-26.8913	78.7011	21.7354
17	1.6761	0.3476	-0.2798	1.4362	-0.3828	1.2872	-0.0244	-0.1377	-0.0908	0.0855	0.0237	-0.1969	-0.0614	-0.1097	-0.0037	0.2584	0.0366	-0.0252	0.1633	0.0319	0.2148	-30.4917	40.6103	20.6224
18	3.3994	-0.5785	0.1802	3.43	0.9537	3.6605	0.0318	0.0085	0.2066	0.0732	0.0646	0.1669	0.0794	-0.0821	-0.1025	0.1477	0.0119	0.0094	0.2757	0.0895	0.2345	-54.1416	47.5205	20.0043
19	2.2491	-0.0428	-0.2138	2.282	-1.2708	3.6043	-0.0225	0.2936	-0.2606	-0.3676	0.051	-0.0498	0.4573	0.0227	-0.0373	0.3397	-0.0001	-0.0049	0.2079	-0.0123	0.184	-44.3659	-1.2407	80.6153
20	2.4075	0.3362	0.0421	0.8628	-0.1901	1.8612	-0.1269	0.5062	0.0712	-0.05	-0.0797	0.0109	0.2428	0.1683	0.1917	0.3266	-0.033	0.0312	0.4607	0.0488	0.1777	-53.4316	17.8385	48.8736

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 428 through 521 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 2 through 199 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 200 through 396 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 397 through 521 )
5	X-RAY DIFFRACTION	5	chain 'E' and (resid 3 through 75 )
6	X-RAY DIFFRACTION	6	chain 'E' and (resid 76 through 227 )
7	X-RAY DIFFRACTION	7	chain 'E' and (resid 228 through 396 )
8	X-RAY DIFFRACTION	8	chain 'E' and (resid 397 through 521 )
9	X-RAY DIFFRACTION	9	chain 'F' and (resid 1 through 199 )
10	X-RAY DIFFRACTION	10	chain 'F' and (resid 200 through 227 )
11	X-RAY DIFFRACTION	11	chain 'F' and (resid 228 through 396 )
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 397 through 521 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 3 through 227 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 228 through 396 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 397 through 521 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 2 through 199 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 200 through 427 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 428 through 521 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 1 through 199 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 200 through 427 )

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Yorodumi