PDB-7sbc: Crystal structure of a GMP synthase from Acinetobacter baumannii ...

ID or keywords:

Entry

Database: PDB / ID: 7sbc

Title

Crystal structure of a GMP synthase from Acinetobacter baumannii AB5075-UW

Components

GMP synthase [glutamine-hydrolyzing]

Keywords

TRANSFERASE / NIAID / ATP-dependent / Gram-negative bacillus / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

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

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of a GMP synthase from Acinetobacter baumannii AB5075-UW
Authors: Edwards, T.E. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	Sep 24, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 6, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7sbc.cif.gz	813.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7sbc.ent.gz	670.2 KB	Display	PDB format
PDBx/mmJSON format	7sbc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7sbc_validation.pdf.gz	473.9 KB	Display	wwPDB validaton report
Full document	7sbc_full_validation.pdf.gz	486.2 KB	Display
Data in XML	7sbc_validation.xml.gz	82.8 KB	Display
Data in CIF	7sbc_validation.cif.gz	123 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sb/7sbc ftp://data.pdbj.org/pub/pdb/validation_reports/sb/7sbc	HTTPS FTP

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Related structure data

Related structure data	1gpmS S: Starting model for refinement
Similar structure data	2ywb-d 20753 6cjq-d 0280 6vxz-d 7482 21453 0279 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: SSGCID-AcbaC.17876.a TargetTrack: AcbaC.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]

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	81.000, 83.180, 104.350
Angle α, β, γ (deg.)	98.910, 109.830, 106.840
Int Tables number	1
Space group name H-M	P1

#1: Protein	GMP synthase [glutamine-hydrolyzing] / GMP synthetase / Glutamine amidotransferase Mass: 59048.117 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: guaA / Production host: Escherichia coli (E. coli) References: UniProt: A0A0R1BBX7, GMP synthase (glutamine-hydrolysing)
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1557 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.58 Å³/Da / Density % sol: 52.24 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: AcbaC.17876.a.B1.PW38920 at 23 mg/mL against MCSG1 condition D3: 0.2 M MgCl2, 30% PEG 400, 0.1 M Tris pH 8.5, direct cryo, unique puck ID ffj4-5, crystal tracking ID 320097d3

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 22, 2021

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.95→48.82 Å / Num. obs: 169147 / % possible obs: 98.4 % / Redundancy: 7.405 % / B_iso Wilson estimate: 25.25 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.056 / R_rim(I) all: 0.06 / Χ²: 0.898 / Net I/σ(I): 23.49 / Num. measured all: 1252528 / Scaling rejects: 4092

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.95-2	6.589	0.458	4.4	80534	12769	12223	0.956	0.497	95.7
2-2.06	7.372	0.355	6.12	89129	12349	12090	0.974	0.381	97.9
2.06-2.12	7.404	0.276	7.71	87553	12066	11825	0.983	0.296	98
2.12-2.18	7.425	0.238	8.73	85467	11727	11511	0.988	0.256	98.2
2.18-2.25	7.433	0.19	10.9	83016	11379	11169	0.991	0.204	98.2
2.25-2.33	7.461	0.173	11.69	79900	10939	10709	0.993	0.186	97.9
2.33-2.42	7.475	0.143	13.77	77825	10533	10412	0.995	0.154	98.9
2.42-2.52	7.497	0.122	15.76	75849	10242	10117	0.996	0.13	98.8
2.52-2.63	7.517	0.101	18.22	72412	9729	9633	0.997	0.108	99
2.63-2.76	7.537	0.084	20.89	69955	9368	9281	0.998	0.091	99.1
2.76-2.91	7.561	0.069	24.64	66603	8868	8809	0.999	0.074	99.3
2.91-3.08	7.582	0.055	29.99	63474	8418	8372	0.999	0.059	99.5
3.08-3.3	7.562	0.043	35.82	59182	7863	7826	0.999	0.046	99.5
3.3-3.56	7.556	0.036	43.35	54920	7339	7268	0.999	0.039	99
3.56-3.9	7.436	0.032	50.84	49965	6778	6719	0.999	0.035	99.1
3.9-4.36	7.334	0.029	58.35	44073	6126	6009	1	0.031	98.1
4.36-5.03	7.326	0.026	64.09	38710	5369	5284	0.999	0.028	98.4
5.03-6.17	7.464	0.028	59.66	33820	4583	4531	0.999	0.03	98.9
6.17-8.72	7.553	0.025	63.7	26231	3508	3473	1	0.027	99
8.72-48.82	7.375	0.02	78.85	13910	1938	1886	0.999	0.022	97.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing
PHENIX	dev-4274	refinement
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1gpm

1gpm

Resolution: 1.95→48.82 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 22.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2085	1935	1.23 %
R_work	0.1774	155730	-
obs	0.1778	157665	91.86 %

Solvent computation

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

Displacement parameters

B_iso max: 104.54 Å² / B_iso mean: 36.132 Å² / B_iso min: 11.7 Å²

Refinement step

Cycle: final / Resolution: 1.95→48.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15577	0	34	1557	17168
B_iso mean	-	-	43.38	37.29	-
Num. residues	-	-	-	-	2011

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.95-2	0.2983	130	0.27	9930	10060	82
2-2.05	0.2427	133	0.2256	10944	11077	91
2.05-2.11	0.2489	147	0.208	11040	11187	91
2.11-2.18	0.2535	142	0.1991	11095	11237	91
2.18-2.26	0.2069	129	0.2059	11112	11241	92
2.26-2.35	0.237	152	0.1971	11115	11267	92
2.35-2.46	0.2322	158	0.1858	11273	11431	93
2.46-2.59	0.2347	154	0.1862	11294	11448	93
2.59-2.75	0.2238	139	0.1884	11353	11492	94
2.75-2.96	0.2069	119	0.1961	11478	11597	94
2.96-3.26	0.2551	123	0.1863	11496	11619	95
3.26-3.73	0.2006	116	0.1686	11415	11531	94
3.73-4.7	0.1627	133	0.1376	10954	11087	91
4.7-48.82	0.1778	160	0.156	11231	11391	93

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	1.3959	-0.0755	0.3757	0.4818	-0.5134	0.8351	-0.0195	0.0638	-0.5931	-0.0101	-0.0418	-0.2843	0.4255	0.1597	0.0725	0.3862	0.0893	0.0523	0.2894	0.0124	0.575	31.0323	-14.2243	-17.3175
2	1.1806	0.3424	0.1428	0.679	0.2758	0.7665	-0.1362	-0.0782	-0.1492	0.0631	0.0715	-0.4633	0.1498	0.4009	0.0658	0.2393	0.0847	0.0641	0.3495	0.0422	0.4763	39.4078	-0.9509	-17.4268
3	0.3795	0.2255	-0.4866	0.4352	-0.0905	1.4381	-0.0421	0.047	-0.0319	-0.0709	0.0038	-0.0085	0.1662	-0.0848	0.0274	0.2637	-0.0649	0.0177	0.2086	-0.0113	0.1758	-1.2911	-9.8203	-11.2198
4	1.1724	0.6452	0.0408	1.2836	0.0463	1.6685	-0.0028	0.0424	0.062	0.0152	-0.0112	0.0638	0.0676	-0.1006	0.0138	0.1482	-0.0122	-0.0015	0.1425	-0.0097	0.1469	3.2525	9.5091	6.1455
5	1.0436	0.0059	-0.1532	1.2096	-0.1308	0.8976	0.0941	-0.0318	-0.4833	0.2757	-0.0751	-0.7111	0.2976	0.3088	-0.0463	0.3575	0.0843	-0.1741	0.3708	0.0541	0.7419	43.4931	16.0938	33.6562
6	0.3862	0.4151	0.0182	0.7422	-0.1079	1.7479	0.0194	-0.0479	-0.0118	0.047	0.0089	-0.0694	-0.1226	0.172	-0.0327	0.2271	-0.0528	0.0014	0.2103	-0.0021	0.1774	37.0155	49.9049	20.3106
7	1.1262	0.3545	-0.3422	1.4331	0.2507	1.6442	-0.0191	0.023	0.0419	-0.0175	0.0213	0.0304	-0.1238	0.0362	-0.0022	0.1557	-0.0091	-0.0118	0.1247	0.0029	0.14	24.0769	36.8375	1.4453
8	0.5729	-0.037	0.4402	1.2535	-0.473	2.0125	0.0221	-0.0466	0.1908	0.088	-0.0687	0.3039	-0.3077	-0.4228	0.0207	0.2137	0.1003	0.0281	0.3179	-0.0463	0.3132	4.5926	51.15	26.1026
9	0.409	0.3982	0.2834	1.1427	0.8887	1.4568	0.1136	-0.1602	-0.0123	0.296	-0.1466	0.0526	0.1599	-0.1111	0.0116	0.2582	-0.0508	-0.0032	0.1834	0.0117	0.1613	11.6414	17.7624	32.8355
10	1.277	0.0848	-0.8042	0.7923	-0.0647	1.657	-0.0151	0.2115	0.2645	-0.0346	0.1775	0.2937	-0.3446	-0.5499	-0.0677	0.32	0.123	-0.0157	0.4376	0.0853	0.3291	-10.3379	19.0453	-24.1382
11	0.8227	0.7426	0.3807	0.8562	0.4397	1.0914	-0.1066	0.1721	0.0093	-0.2544	0.1081	-0.0286	-0.1581	0.1456	-0.0044	0.3078	-0.0534	0.0317	0.2561	-0.0069	0.1786	22.4223	20.4034	-33.2247
12	0.9146	0.43	-0.2647	1.4511	0.1286	1.5383	-0.0355	0.1116	-0.037	-0.0763	0.0413	0.0086	0.0142	0.0928	-0.0084	0.1608	-0.012	0.0028	0.176	-0.0189	0.1893	27.3837	24.9662	-9.4422

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 98 )	A	4 - 98
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 99 through 206 )	A	99 - 206
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 207 through 414 )	A	207 - 414
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 415 through 522 )	A	415 - 522
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 4 through 206 )	B	4 - 206
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 207 through 414 )	B	207 - 414
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 415 through 522 )	B	415 - 522
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 0 through 234 )	C	0 - 234
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 235 through 522 )	C	235 - 522
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 0 through 234 )	D	0 - 234
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 235 through 414 )	D	235 - 414
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 415 through 522 )	D	415 - 522

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