PDB-4kzt: Structure mmNAGS bound with L-arginine

ID or keywords:

Entry

Database: PDB / ID: 4kzt

Title

Structure mmNAGS bound with L-arginine

Components

N-acetylglutamate kinase / N-acetylglutamate synthase

Keywords

TRANSFERASE/TRANSFERASE INHIBITOR / synthetase /

kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex

Function / homology

Function and homology information

acetylglutamate kinase /

acetylglutamate kinase activity / arginine biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups /

phosphorylation /

cytoplasm
Similarity search - Function

Biological species

Maricaulis maris (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.8 Å

Authors

Zhao, G. / Jin, Z. / Allewell, N.M. / Tuchman, M. / Shi, D.

Citation

Journal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Structure of N-acetyl-L-glutamate synthase/kinase from Maricaulis maris with the allosteric inhibitor L-arginine bound.
Authors: Zhao, G. / Haskins, N. / Jin, Z. / M Allewell, N. / Tuchman, M. / Shi, D.

History

Deposition	May 30, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 16, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.2	Sep 20, 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 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4kzt.cif.gz	685.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4kzt.ent.gz	578 KB	Display	PDB format
PDBx/mmJSON format	4kzt.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/kz/4kzt ftp://data.pdbj.org/pub/pdb/validation_reports/kz/4kzt	HTTPS FTP

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Related structure data

Related structure data	3s6hS S: Starting model for refinement
Similar structure data	3s6g-d 3s6h-d 3s7y-1 6vzu-d 3qdk-d 6vzv-d 6vzs-d 5cox-d 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	#133 - Jan 2011 Nitric Oxide Synthase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (3) #97 - Jan 2008 Circadian Clock Proteins similarity (3)

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

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	165.829, 110.823, 117.196
Angle α, β, γ (deg.)	90.000, 91.020, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	N-acetylglutamate kinase / N-acetylglutamate synthase Mass: 50232.758 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): BL21(DE3) References: UniProt: Q0ASS9, amino-acid N-acetyltransferase, acetylglutamate kinase
#2: Chemical	ChemComp-ARG / ARGININE / Arginine Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₅N₄O₂
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.68 Å³/Da / Density % sol: 54.09 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 100 mM cacodylic acid sodium salt trihydrate, pH 6.2, 25% polypropylene glycol P400 and 200 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 298 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 26, 2011

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Redundancy: 6.6 % / Av σ(I) over netI: 36.98 / Number: 312380 / R_merge(I) obs: 0.081 / Χ²: 2.37 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 47676 / % possible obs: 90.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
7.59	50	96.9	1	0.048	3.699	6.4
6.03	7.59	99.9	1	0.056	3.458	7.1
5.27	6.03	100	1	0.064	3.336	7.2
4.79	5.27	99.9	1	0.065	3.479	7.1
4.44	4.79	100	1	0.071	3.385	7.2
4.18	4.44	100	1	0.08	3.047	7.4
3.97	4.18	100	1	0.099	2.828	7.5
3.8	3.97	100	1	0.123	2.466	7.6
3.65	3.8	100	1	0.145	2.198	7.6
3.53	3.65	100	1	0.168	1.961	7.6
3.42	3.53	99.9	1	0.206	1.694	7.4
3.32	3.42	99.9	1	0.25	1.483	7.1
3.23	3.32	98.7	1	0.284	1.391	6.6
3.15	3.23	94.6	1	0.341	1.26	6.1
3.08	3.15	86.8	1	0.406	1.245	5.8
3.02	3.08	79	1	0.469	1.216	5.4
2.96	3.02	72.5	1	0.486	1.162	4.7
2.9	2.96	64.2	1	0.596	1.213	4.1
2.85	2.9	57.8	1	0.58	1.16	3.5
2.8	2.85	54.1	1	0.656	1.137	2.9

Reflection

Resolution: 2.8→50 Å / Num. all: 52797 / Num. obs: 47676 / % possible obs: 90.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / R_merge(I) obs: 0.081 / Χ²: 2.365 / Net I/σ(I): 13.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.8-2.85	2.9	0.656	1431	1.137	1	54.1
2.85-2.9	3.5	0.58	1490	1.16	1	57.8
2.9-2.96	4.1	0.596	1707	1.213	1	64.2
2.96-3.02	4.7	0.486	1913	1.162	1	72.5
3.02-3.08	5.4	0.469	2052	1.216	1	79
3.08-3.15	5.8	0.406	2288	1.245	1	86.8
3.15-3.23	6.1	0.341	2504	1.26	1	94.6
3.23-3.32	6.6	0.284	2579	1.391	1	98.7
3.32-3.42	7.1	0.25	2617	1.483	1	99.9
3.42-3.53	7.4	0.206	2639	1.694	1	99.9
3.53-3.65	7.6	0.168	2644	1.961	1	100
3.65-3.8	7.6	0.145	2619	2.198	1	100
3.8-3.97	7.6	0.123	2646	2.466	1	100
3.97-4.18	7.5	0.099	2649	2.828	1	100
4.18-4.44	7.4	0.08	2630	3.047	1	100
4.44-4.79	7.2	0.071	2664	3.385	1	100
4.79-5.27	7.1	0.065	2636	3.479	1	99.9
5.27-6.03	7.2	0.064	2652	3.336	1	100
6.03-7.59	7.1	0.056	2672	3.458	1	99.9
7.59-50	6.4	0.048	2644	3.699	1	96.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3S6H

3s6h

Resolution: 2.8→39.298 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7188 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 33.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2654	1998	4.2 %	RANDOM
R_work	0.1957	-	-	-
all	0.1987	53056	-	-
obs	0.1986	47618	89.75 %	-

Solvent computation

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

Displacement parameters

B_iso max: 242.21 Å² / B_iso mean: 102.4575 Å² / B_iso min: 33.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→39.298 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13244	0	76	18	13338

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	13544
X-RAY DIFFRACTION	f_angle_d	1.354	18376
X-RAY DIFFRACTION	f_chiral_restr	0.086	2096
X-RAY DIFFRACTION	f_plane_restr	0.007	2428
X-RAY DIFFRACTION	f_dihedral_angle_d	15.266	4976

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / 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 (%)
2.8-2.8568	0.4829	81	0.3784	1869	1950	52
2.8568-2.934	0.4057	102	0.3265	2208	2310	61
2.934-3.0203	0.3912	119	0.2781	2584	2703	72
3.0203-3.1178	0.3229	129	0.268	2966	3095	82
3.1178-3.2292	0.3326	144	0.2599	3375	3519	93
3.2292-3.3584	0.3426	156	0.2526	3590	3746	99
3.3584-3.5112	0.2944	154	0.2328	3590	3744	100
3.5112-3.6961	0.2802	160	0.2052	3642	3802	100
3.6961-3.9275	0.2827	157	0.191	3604	3761	100
3.9275-4.2304	0.2347	161	0.1775	3624	3785	100
4.2304-4.6556	0.2301	156	0.1565	3643	3799	100
4.6556-5.3278	0.2306	160	0.1649	3640	3800	100
5.3278-6.7071	0.29	162	0.2142	3656	3818	100
6.7071-39.298	0.2258	157	0.1705	3629	3786	97

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	4.8457	2.5171	-3.0955	3.795	2.1075	7.5295	-0.0363	0.0617	1.4296	0.4808	0.4557	-0.892	-2.3276	1.8042	-0.6101	1.8137	-0.1966	-0.4536	0.8691	-0.0416	1.045	128.6555	139.9926	-20.7427
2	6.837	1.0101	-0.6976	3.7623	-1.0195	3.0352	0.0685	-0.1041	0.1064	-0.0332	0.1608	0.5356	0.0296	-0.7235	-0.2803	1.0138	0.0621	-0.1513	0.6263	0.0976	0.6314	98.8491	143.9327	-21.1451
3	7.6308	1.7919	-1.5975	6.6148	-2.7015	7.2868	-0.0471	-0.9845	-0.1819	1.367	-0.1249	0.4304	-0.2569	-0.3708	0.0717	1.3433	0.0945	-0.1577	0.5943	0.0391	0.54	110.6284	129.3943	-9.0332
4	7.6919	0.6502	2.9932	4.6835	0.1214	5.3715	0.1225	0.4461	-0.7858	0.9984	0.1441	-0.1084	1.5941	0.5474	-0.2437	1.74	0.2119	-0.1057	0.5407	0.0156	0.6904	128.9505	112.5995	-5.8343
5	3.627	-1.4911	3.9746	5.4303	-1.9061	5.1162	0.6038	-0.098	-0.5348	1.7826	-0.2273	-0.7821	0.5213	0.4442	-0.3275	1.8778	0.0315	-0.3921	0.6889	0.0829	0.6543	136.3162	121.0913	6.3837
6	6.2456	2.8463	2.5306	7.2584	-2.793	3.637	-0.2656	-1.6892	0.4003	-0.2139	-0.3969	-2.1561	0.2954	2.4236	1.1519	0.7467	0.2186	-0.1207	1.5202	-0.0561	1.4787	118.393	175.8366	-40.2115
7	7.3163	0.9474	-0.5971	5.8879	0.1333	4.739	-0.147	-0.3494	-0.724	0.1374	0.1797	0.1869	1.2266	-0.4211	-0.0147	0.9594	0.0695	-0.0704	0.6208	0.1408	0.5666	95.7774	155.4677	-40.3889
8	7.9861	-2.1579	5.8282	5.5018	-1.8013	8.5341	0.0655	0.5436	0.3266	-0.1521	-0.1775	-0.1821	0.4085	0.5449	0.1334	0.4294	0.0065	0.0017	0.3968	-0.0016	0.4638	97.8663	173.9861	-52.4991
9	2.1796	0.1621	-1.7157	9.0179	-0.7982	7.1993	0.3215	0.0069	0.6988	0.3356	0.1268	0.3167	-0.3187	-0.088	-0.3789	0.5279	-0.012	-0.1383	0.5148	-0.0607	1.1234	103.4463	198.1691	-55.5329
10	8.1502	0.1662	-4.7935	8.2659	-1.7229	7.749	0.5031	0.2367	1.6722	-0.3374	-0.1867	-0.2901	-0.1953	0.4797	-0.2354	0.642	-0.0623	-0.178	0.4668	0.0393	1.0658	113.5011	194.8056	-68.3718
11	3.8994	4.394	-0.5103	4.9634	-0.5987	2.6594	-0.3546	0.3588	1.24	-0.9634	-0.1356	2.3922	0.2026	-0.8063	0.3906	1.4447	-0.0178	-0.2881	1.0536	-0.2515	1.188	128.1454	155.2644	-10.904
12	4.5493	0.1771	-1.0131	3.215	-1.5225	6.6608	-0.0433	0.2782	0.1549	0.0412	-0.592	-0.8672	-0.3552	1.2773	0.6123	1.4543	0.0781	-0.3544	1.0303	0.0912	0.8044	155.3912	159.5446	-23.6183
13	5.87	0.4789	0.4878	6.2687	0.1026	9.6326	0.3812	-0.7509	-0.6573	0.0979	-0.6682	-0.6864	0.3271	1.2718	0.2388	1.2168	-0.034	-0.2315	0.9086	0.0871	0.6348	150.6439	150.9354	-3.6144
14	6.2484	1.425	1.4722	6.2339	1.6199	6.0531	0.1568	-0.7408	0.4426	1.4116	-0.2753	0.2434	-0.1635	0.2748	0.4742	1.8356	0.0518	-0.3034	0.8502	-0.1598	0.4893	137.9285	150.2761	18.2024
15	4.8655	0.8102	-0.7779	3.3602	-1.8471	5.6212	0.4768	-0.5984	-0.0017	1.2635	-0.099	-0.1747	0.727	-0.1868	-0.0817	1.8997	-0.0717	-0.2886	0.9006	0.063	0.399	132.9612	134.5301	16.4195
16	1.8502	1.4989	-1.6	5.3019	-2.5514	6.0083	0.323	-0.4724	-0.1256	1.3774	0.7949	1.0582	-0.2906	-2.4148	-0.9419	1.2182	0.2405	0.1228	1.4502	0.2741	1.1411	125.2056	163.7239	-51.4651
17	7.5015	2.4529	-0.98	4.5357	-1.1605	6.6255	0.0525	-0.5102	0.791	0.4249	-0.593	-0.4827	-1.0171	1.2389	0.6358	1.5312	0.1416	-0.3003	0.9915	0.0692	0.7332	151.3639	174.0668	-40.6593
18	6.4856	1.6745	-1.6722	8.2161	-1.473	9.3725	-0.5568	0.1348	1.0785	0.4347	0.2629	-0.3042	-1.3129	0.2067	0.1116	1.394	0.2376	-0.2701	0.6354	0.0181	0.6394	142.1147	178.2848	-60.4399
19	6.4069	-2.02	-0.7577	7.1356	1.4656	4.3015	-0.2882	0.2931	-0.4497	-0.7209	0.0455	-0.3341	1.3301	-0.1613	-0.0186	1.5782	-0.1241	-0.0938	0.5006	-0.0445	0.4586	129.7468	171.355	-81.275
20	4.2245	-2.0956	-1.5686	8.958	2.9413	9.1441	0.099	0.504	0.227	-0.716	0.1703	0.5984	0.2653	-0.676	-0.3788	0.9512	-0.1179	-0.1843	0.5936	0.0907	0.5139	117.1535	181.7988	-78.8572

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

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Structure visualization

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi