PDB-3s6g: Crystal structures of Seleno-substituted mutant mmNAGS in space g...

ID or keywords:

Entry

Database: PDB / ID: 3s6g

Title

Crystal structures of Seleno-substituted mutant mmNAGS in space group P212121

Components

N-acetylglutamate kinase / N-acetylglutamate synthase

Keywords

TRANSFERASE / synthase / kinase

Function / homology

Function and homology information

acetylglutamate kinase / acetylglutamate kinase activity / acetyl-CoA:L-glutamate N-acetyltransferase activity / N-acetyl-gamma-glutamyl-phosphate reductase activity / glutamate metabolic process / arginine biosynthetic process / phosphorylation / cytoplasm
Similarity search - Function

Biological species

Maricaulis maris (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.6681 Å

Authors

Shi, D. / Li, Y. / Cabrera-Luque, J. / Jin, Z. / Yu, X. / Allewell, N.M. / Tuchman, M.

Citation

Journal: Plos One / Year: 2011
Title: A Novel N-acetylglutamate synthase architecture revealed by the crystal structure of the bifunctional enzyme from Maricaulis maris.
Authors: Shi, D. / Li, Y. / Cabrera-Luque, J. / Jin, Z. / Yu, X. / Zhao, G. / Haskins, N. / Allewell, N.M. / Tuchman, M.

History

Deposition	May 25, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 18, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3s6g.cif.gz	671.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3s6g.ent.gz	580.6 KB	Display	PDB format
PDBx/mmJSON format	3s6g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3s6g_validation.pdf.gz	734.3 KB	Display	wwPDB validaton report
Full document	3s6g_full_validation.pdf.gz	797.6 KB	Display
Data in XML	3s6g_validation.xml.gz	65.6 KB	Display
Data in CIF	3s6g_validation.cif.gz	88.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s6/3s6g ftp://data.pdbj.org/pub/pdb/validation_reports/s6/3s6g	HTTPS FTP

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Related structure data

Related structure data	3s6hC 3s6kC 3s7yC C: citing same article (ref.)
Similar structure data	4kzt-d 3s6h-d 3s7y-1 4ab7-1 6vzu-d 3qdk-d 6o0e-d 6o0d-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) 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	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #97 - Jan 2008 Circadian Clock Proteins similarity (3) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

Deposited unit

A: N-acetylglutamate kinase / N-acetylglutamate synthase

B: N-acetylglutamate kinase / N-acetylglutamate synthase

X: N-acetylglutamate kinase / N-acetylglutamate synthase

Y: N-acetylglutamate kinase / N-acetylglutamate synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

A: N-acetylglutamate kinase / N-acetylglutamate synthase

X: N-acetylglutamate kinase / N-acetylglutamate synthase

hetero molecules

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

3

B: N-acetylglutamate kinase / N-acetylglutamate synthase

Y: N-acetylglutamate kinase / N-acetylglutamate synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	113.426, 117.470, 149.297
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABXY

#1: Protein	N-acetylglutamate kinase / N-acetylglutamate synthase Mass: 50526.684 Da / Num. of mol.: 4 / Mutation: I106M, I294M, L376M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Maricaulis maris (bacteria) / Strain: MCS10 / Gene: argA/B, Mmar10_0365 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) References: UniProt: Q0ASS9, amino-acid N-acetyltransferase, acetylglutamate kinase

#1: Protein

N-acetylglutamate kinase / N-acetylglutamate synthase

Mass: 50526.684 Da / Num. of mol.: 4 / Mutation: I106M, I294M, L376M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Maricaulis maris (bacteria) / Strain: MCS10 / Gene: argA/B, Mmar10_0365 / Plasmid: pET28a / Production host:

Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q0ASS9, amino-acid N-acetyltransferase, acetylglutamate kinase

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Non-polymers , 5 types, 90 molecules

#2: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₂O₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.46 Å³/Da / Density % sol: 50.01 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 25% PEG3350, 200 mM sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 298 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 0.97471, 0.97921, 0.97934

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 23, 2010

Radiation

Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97471	1
2	0.97921	1
3	0.97934	1

Reflection

Resolution: 2.66→50 Å / Num. obs: 104589 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / R_merge(I) obs: 0.072 / Net I/σ(I): 36.8

Reflection shell

Resolution: 2.66→2.73 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.577 / Mean I/σ(I) obs: 2.6 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
PHENIX	1.6.4_486	refinement
PDB_EXTRACT	3.1	data extraction
DENZO		data reduction
SCALEPACK		data scaling
HKL-2000		data scaling
SHELXS		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.6681→37.969 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.32 / Isotropic thermal model: Isotropic / σ(F): 0 / Phase error: 27.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2556	3690	3.53 %
R_work	0.1826	-	-
obs	0.1851	104589	95.4 %
all	-	109628	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 44.721 Å² / k_sol: 0.31 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.9617 Å²	-0 Å²	0 Å²
2-	-	-5.3741 Å²	-0 Å²
3-	-	-	12.3358 Å²

Refinement step

Cycle: LAST / Resolution: 2.6681→37.969 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13136	0	75	84	13295

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	13450
X-RAY DIFFRACTION	f_angle_d	1.21	18278
X-RAY DIFFRACTION	f_dihedral_angle_d	16.882	4962
X-RAY DIFFRACTION	f_chiral_restr	0.08	2088
X-RAY DIFFRACTION	f_plane_restr	0.007	2409

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 (%)
2.6681-2.7635	0.3252	333	0.2764	8634	X-RAY DIFFRACTION	82
2.7635-2.8741	0.3468	338	0.2556	9469	X-RAY DIFFRACTION	89
2.8741-3.0048	0.3414	354	0.2457	9666	X-RAY DIFFRACTION	92
3.0048-3.1632	0.3102	371	0.2226	10130	X-RAY DIFFRACTION	96
3.1632-3.3613	0.2846	374	0.2134	10363	X-RAY DIFFRACTION	98
3.3613-3.6206	0.2647	389	0.1906	10439	X-RAY DIFFRACTION	99
3.6206-3.9846	0.2479	388	0.1723	10492	X-RAY DIFFRACTION	99
3.9846-4.5604	0.2186	372	0.142	10605	X-RAY DIFFRACTION	100
4.5604-5.7424	0.2403	384	0.1582	10534	X-RAY DIFFRACTION	100
5.7424-37.9729	0.2277	387	0.175	10567	X-RAY DIFFRACTION	100

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	0.4992	-0.9278	-0.5172	3.1757	-0.2094	2.4658	0.1379	0.012	-0.0393	-0.419	0.298	-0.6433	-0.3095	0.3466	-0.4241	0.5744	0.0354	0.2474	0.2898	0.0544	0.5237	39.6307	-4.0201	76.3596
2	1.9518	0.0528	0.3583	1.099	0.5571	1.9284	0.0038	-0.3203	-0.2026	0.083	0.0649	-0.2413	0.0936	0.6674	-0.1337	0.2346	0.0764	-0.0043	0.4889	-0.1327	0.3404	43.9491	-6.4165	105.6313
3	7.1683	2.4465	-2.0028	2.5966	1.0476	2.2938	0.1721	-0.2603	-0.8339	0.0828	-0.0757	-0.2762	0.6903	-0.1181	-0.0536	0.4566	0.0079	-0.0262	0.2592	-0.0091	0.3202	26.9929	-16.0319	95.3151
4	1.4033	-0.8511	-0.7809	2.2494	1.0354	1.4251	-0.1168	0.0797	0.129	0.0109	0.1956	0.3961	0.0572	-0.1839	-0.0129	0.0917	-0.1104	0.0287	0.109	-0.0086	0.3137	7.3638	-15.8654	78.9031
5	3.8808	-2.5434	-0.3597	2.1372	0.6559	2.3327	0.2803	0.5881	-0.4204	-0.1795	-0.1872	-0.1851	0.1328	0.222	-0.0457	0.2498	-0.1361	0.0219	0.4093	-0.1212	0.4137	10.8407	-29.4844	70.3854
6	6.1764	-2.5998	-1.5347	4.2645	-4.2837	8.5048	0.0389	0.0432	-1.4722	-0.9492	-1.0182	0.0199	0.6434	1.6011	0.3906	0.9985	0.1821	-0.4395	0.7446	-0.2468	1.102	77.1893	8.7047	81.2783
7	4.3963	1.7679	-0.6802	1.6157	-1.5539	0.9828	-0.3801	-0.2784	0.5381	0.1246	0.0843	0.101	0.3833	0.1425	0.1439	0.6025	-0.1715	-0.239	0.5997	0.137	0.437	58.717	11.3952	107.0387
8	4.5646	1.8932	0.393	1.5533	0.1073	1.2326	-0.1999	-0.4284	0.6823	-0.0285	-0.0729	0.2255	-0.2835	0.0816	0.2415	0.629	-0.1458	-0.2462	0.5982	0.0709	0.6528	78.1864	21.6717	103.0742
9	1.8762	-0.9931	0.0903	2.8224	-1.8899	3.0347	-0.3603	-0.5005	-0.2266	-0.075	0.0964	-0.9213	0.0953	0.4476	0.2843	0.4361	0.0389	-0.1982	0.5395	0.1864	0.887	101.7672	22.8696	94.5231
10	2.1803	-2.1699	1.6546	3.0327	-2.3224	1.6977	-0.0074	0.0356	0.3285	0.3346	-0.0702	-0.4762	0.0336	0.4098	0.1302	0.3702	-0.0226	-0.1301	0.4144	0.1035	0.669	98.36	35.0177	83.909
11	0.9708	0.1138	-0.4737	2.7658	1.8243	2.1961	-0.473	-0.0746	-0.145	-0.0153	-0.3673	0.5187	-0.0818	-0.2607	0.4819	0.5674	0.2904	-0.1566	0.6669	0.0662	0.5897	50.3503	-17.8683	73.4201
12	2.7626	0.846	-2.6472	3.6175	-1.0872	2.4316	-0.1713	0.3076	0.0106	-0.4778	0.1829	0.2352	0.1463	-0.2524	-0.0023	0.1895	-0.0617	0.0279	0.2049	-0.0954	0.1276	50.774	-6.4539	45.1849
13	2.1701	3.4116	-0.0107	7.3904	1.1366	0.274	-0.3066	0.1373	-0.0417	-0.3457	0.1604	0.5572	-0.0249	-0.2954	0.1068	0.4065	-0.0233	0.011	0.418	-0.0772	0.3102	38.9027	-24.4708	51.3111
14	3.8115	-0.5584	-0.7015	1.7616	0.687	4.8596	0.1318	0.1751	-0.9309	-0.1311	-0.0188	-0.1225	0.2719	0.1079	-0.1104	0.1801	-0.0175	-0.0039	0.1181	-0.007	0.491	36.2872	-46.6986	63.4434
15	2.8234	-1.0345	-1.5093	4.4528	-0.8996	1.3309	0.2003	0.1359	-0.1782	0.3563	-0.3746	0.8062	-0.0623	0.1602	0.1362	0.2713	-0.1687	0.112	0.2888	-0.1441	0.5199	22.4333	-42.3789	71.5372
16	7.5644	-2.9484	1.8519	1.5551	-0.5496	0.4327	-1.8252	-0.342	0.7368	1.2379	0.9406	0.8483	-0.2419	-0.7896	0.7243	1.5523	0.2205	0.1392	1.2659	-0.0542	0.8328	67.987	20.5802	74.9256
17	2.2071	1.1311	0.1188	4.1711	0.2039	1.4412	-0.0739	0.1063	-0.1945	0.2991	0.1495	-0.5061	0.5011	0.0493	-0.044	0.4811	-0.0232	-0.089	0.2266	-0.0627	0.4071	69.8462	6.4188	46.4438
18	1.4924	2.3943	0.821	4.7435	0.7992	1.0614	-0.2352	-0.0333	-0.3462	0.2831	0.5728	-0.7833	-0.2057	0.5006	-0.3754	0.4608	-0.0595	-0.0269	0.4456	-0.2115	0.6449	79.6403	25.1472	52.685
19	2.0615	-1.218	0.617	2.0287	-1.7978	4.1906	0.0444	0.1615	0.1348	-0.1576	0.0746	0.2882	0.3631	-0.1358	-0.1008	0.3073	0.0018	-0.079	0.1868	-0.051	0.6045	73.9855	47.0461	68.0939
20	3.2542	-1.488	0.966	1.6965	-1.6517	2.8131	-0.0871	-0.0156	0.1055	0.422	-0.1463	-0.5807	0.0306	-0.0388	0.251	0.4299	-0.0487	-0.1013	0.2069	-0.0009	0.5706	85.0969	45.6716	80.4602

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 5:35)
2	X-RAY DIFFRACTION	2	(chain A and resid 36:204)
3	X-RAY DIFFRACTION	3	(chain A and resid 205:291)
4	X-RAY DIFFRACTION	4	(chain A and resid 292:381)
5	X-RAY DIFFRACTION	5	(chain A and resid 382:440)
6	X-RAY DIFFRACTION	6	(chain B and resid 5:35)
7	X-RAY DIFFRACTION	7	(chain B and resid 36:204)
8	X-RAY DIFFRACTION	8	(chain B and resid 205:291)
9	X-RAY DIFFRACTION	9	(chain B and resid 292:381)
10	X-RAY DIFFRACTION	10	(chain B and resid 382:439)
11	X-RAY DIFFRACTION	11	(chain X and resid 5:35)
12	X-RAY DIFFRACTION	12	(chain X and resid 36:204)
13	X-RAY DIFFRACTION	13	(chain X and resid 205:291)
14	X-RAY DIFFRACTION	14	(chain X and resid 292:381)
15	X-RAY DIFFRACTION	15	(chain X and resid 382:439)
16	X-RAY DIFFRACTION	16	(chain Y and resid 10:31)
17	X-RAY DIFFRACTION	17	(chain Y and resid 40:204)
18	X-RAY DIFFRACTION	18	(chain Y and resid 205:291)
19	X-RAY DIFFRACTION	19	(chain Y and resid 292:381)
20	X-RAY DIFFRACTION	20	(chain Y and resid 382:440)

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