PDB-3d2p: Crystal structure of N-acetylglutamate synthase from Neisseria go...

ID or keywords:

Entry

Database: PDB / ID: 3d2p

Title

Crystal structure of N-acetylglutamate synthase from Neisseria gonorrhoeae complexed with coenzyme A and L-arginine

Components

Putative acetylglutamate synthase

Keywords

TRANSFERASE / Protein-CoA-Arg ternary complex

Function / homology

Function and homology information

methione N-acyltransferase activity /

amino-acid N-acetyltransferase /

acetyl-CoA:L-glutamate N-acetyltransferase activity / arginine biosynthetic process /

cytoplasm
Similarity search - Function

Biological species

Neisseria gonorrhoeae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.56 Å

Authors

Shi, D. / Min, L. / Jin, Z. / Allewell, N.M. / Tuchman, M.

Citation

Journal: J.Biol.Chem. / Year: 2009
Title: Mechanism of Allosteric Inhibition of N-Acetyl-L-glutamate Synthase by L-Arginine.
Authors: Min, L. / Jin, Z. / Caldovic, L. / Morizono, H. / Allewell, N.M. / Tuchman, M. / Shi, D.

History

Deposition	May 8, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 23, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3d2p.cif.gz	180.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3d2p.ent.gz	142.7 KB	Display	PDB format
PDBx/mmJSON format	3d2p.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/d2/3d2p ftp://data.pdbj.org/pub/pdb/validation_reports/d2/3d2p	HTTPS FTP

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Related structure data

Related structure data	3d2mC 2r8vS 3b8g S: Starting model for refinement C: citing same article (ref.)
Similar structure data	0364 4889 3tdk-1 11840 3j94-d 1do2-1 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	#133 - Jan 2011 Nitric Oxide Synthase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (5) #97 - Jan 2008 Circadian Clock Proteins similarity (4) #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: Putative acetylglutamate synthase

B: Putative acetylglutamate synthase

hetero molecules

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

1

A: Putative acetylglutamate synthase

B: Putative acetylglutamate synthase

hetero molecules

A: Putative acetylglutamate synthase

B: Putative acetylglutamate synthase

hetero molecules

A: Putative acetylglutamate synthase

B: Putative acetylglutamate synthase

hetero molecules

defined by author&software
301 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	107.054, 107.054, 185.466
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	149
Space group name H-M	P312

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B
3	3	A

NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	ARG	ARG	6	A	A	5 - 436	25 - 456
2	1	ASP	ASP	ARG	ARG	6	B	B	5 - 436	25 - 456
1	2	ARG	ARG	ARG	ARG	4	A	D	438
2	2	ARG	ARG	ARG	ARG	4	B	F	438
1	3	COA	COA	COA	COA	1	A	C	437
2	3	COA	COA	COA	COA	1	B	E	437

NCS ensembles :

ID
1
2
3

#1: Protein	Putative acetylglutamate synthase Mass: 49235.492 Da / Num. of mol.: 2 / Mutation: V312I, D336N, P427S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: ATCC53420 / Gene: argA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5FAK7, amino-acid N-acetyltransferase
#2: Chemical	ChemComp-COA / COENZYME A / Coenzyme A Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#3: Chemical	ChemComp-ARG / ARGININE / Arginine Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₅N₄O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.12 Å³/Da / Density % sol: 60.52 %
Crystal grow	Temperature: 291 K / Method: evaporation / pH: 6.4 Details: 8% PEG3350, 100 mM ammonium citrate , pH 6.4, EVAPORATION, temperature 291K

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Data collection

Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 19, 2008
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.56→185.7 Å / Num. all: 39196 / Num. obs: 35747 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / R_merge(I) obs: 0.115 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2.56→2.63 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.701 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3330 / % possible all: 86.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
CBASS		data collection
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2R8V

2r8v

Resolution: 2.56→20 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.878 / SU B: 21.176 / SU ML: 0.231 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.359 / ESU R: 0.566 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27252	1786	5 %	RANDOM
R_work	0.21378	-	-	-
obs	0.21667	33955	90.76 %	-
all	-	37231	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 29.582 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.24 Å²	-0.12 Å²	0 Å²
2-	-	-0.24 Å²	0 Å²
3-	-	-	0.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.56→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6446	0	120	179	6745

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.021	6676
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.8	1.974	9040
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.635	5	842
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.278	22.467	300
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.783	15	1078
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.171	15	70
X-RAY DIFFRACTION	r_chiral_restr	0.116	0.2	1028
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5054
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.262	0.2	3219
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.321	0.2	4532
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.188	0.2	267
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	0.249	0.2	120
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.181	0.2	9
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	0.628	1.5	4264
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.11	2	6644
X-RAY DIFFRACTION	r_scbond_it	2.056	3	2642
X-RAY DIFFRACTION	r_scangle_it	3.257	4.5	2396
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Number	Type	Rms dev position (Å)	Weight position
3	3	48	tight positional	0.05	0.05
2	2	12	medium positional	0.12	0.5
1	1	3223	loose positional	0.37	5
3	3	48	tight thermal	0.23	0.5
2	2	12	medium thermal	0.74	2
1	1	3223	loose thermal	2.06	10

LS refinement shell

Resolution: 2.56→2.63 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.386	122	-
R_work	0.357	2157	-
obs	-	3330	79.21 %

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	0.1003	0.6446	0.0785	6.4336	1.2281	1.1669	-0.1249	-0.0068	-0.0087	-0.15	0.1192	-0.3586	-0.0644	0.2161	0.0057	-0.0419	-0.0249	0.1107	0.0413	0.0615	-0.0155	-21.7228	32.5713	43.4041
2	13.332	-4.8236	0.1918	15.8491	-2.6983	12.3888	-0.1135	-0.3077	-0.9991	-0.2438	-0.1263	-1.3102	0.9398	0.9982	0.2398	0.1377	0.1697	0.2113	0.1428	-0.008	0.4168	-9.0718	5.6414	36.6748
3	2.7369	0.7	-0.7547	7.9552	5.923	8.1539	-0.0867	0.383	-0.2083	-0.4715	-0.1363	-0.1435	-0.0668	-0.1187	0.223	-0.0597	0.091	0.0774	0.0438	0.0784	0.074	-18.2994	10.6822	41.0813
4	1.7633	0.495	0.5079	2.2672	0.3198	1.295	-0.014	0.2982	-0.1036	-0.2692	-0.0578	-0.0645	0.1979	0.0593	0.0718	0.0126	0.0061	0.1063	-0.0013	0.0244	-0.0332	-27.9947	16.2372	36.0571
5	14.1433	-0.8445	4.852	5.9975	4.0449	4.8239	-0.1624	0.4982	-0.6572	-0.6837	0.1421	-0.9235	0.1937	0.6294	0.0203	0.295	-0.1118	0.1963	0.255	0.0923	0.1676	-10.9172	28.5227	23.1676
6	0.8565	-1.6201	-0.6484	6.1507	-0.4204	1.3698	-0.0771	0.1763	-0.0541	-0.3645	0.0548	0.0551	-0.167	0.0019	0.0223	0.0255	-0.0597	0.0919	0.1145	0.088	-0.0195	-22.237	38.371	29.5398
7	8.2671	0.4488	-0.4063	0.4412	2.3918	13.9993	0.4009	-1.0426	2.0193	-0.1576	-0.074	-0.7038	-0.876	0.0932	-0.3268	0.5564	-0.1484	0.2195	0.4419	0.145	0.6367	-27.0925	67.557	28.6731
8	5.3488	-1.1792	-1.6915	4.0687	1.028	2.0029	0.3213	0.6942	0.5522	-1.0961	-0.157	0.0135	-0.5771	-0.3481	-0.1643	0.4472	-0.0298	0.0526	0.3016	0.1243	0.0475	-27.901	59.4914	19.1626
9	7.488	-2.2406	3.1983	9.4556	-2.4925	9.9989	0.314	0.6331	0.1532	-0.9873	0.0269	-0.5164	-0.9324	0.1117	-0.3408	0.5797	-0.0522	0.3225	0.3147	0.032	0.2451	-20.4428	58.4112	13.6184
10	4.7206	-3.7595	-1.1197	3.8044	0.4551	0.5099	-0.0677	0.6207	0.5568	-0.9899	0.1586	-0.6227	-0.3839	-0.1001	-0.0909	1.0344	-0.041	0.1921	0.6262	0.1888	0.6796	-18.7511	70.0325	9.6748
11	7.0029	1.9429	1.0132	0.6339	0.6102	1.2888	0.1169	0.0397	-0.3883	-0.1449	-0.0261	-0.0625	0.1283	-0.0163	-0.0908	0.043	0.0137	0.041	-0.1025	0.0481	-0.0155	-46.7227	-0.1043	50.8865
12	15.2326	-5.4092	-10.3569	13.2802	2.2065	13.8135	-0.799	-0.1962	-0.2695	-0.2699	0.4817	-0.6453	0.9615	0.9457	0.3173	0.0729	0.0757	0.0957	0.0731	0.0826	0.198	-17.3475	-5.0293	57.8454
13	4.943	1.8856	3.2808	3.262	1.0893	7.8505	-0.1746	-0.0078	-0.0701	0.1675	-0.0752	-0.3204	-0.263	0.1397	0.2498	0.01	0.0891	0.1627	-0.1465	0.0111	0.0624	-24.6428	2.3674	53.3207
14	2.4754	0.5334	0.933	1.8626	0.2187	1.5811	-0.0457	0.0742	-0.0067	0.1072	-0.0257	-0.0749	-0.0209	0.1808	0.0713	-0.1026	0.0156	0.0787	-0.0998	0.0316	-0.0212	-32.6257	10.2793	58.2089
15	7.8978	-2.8572	4.6126	10.1379	4.9915	7.5662	0.401	-0.3168	-0.9403	0.8018	0.0264	-0.5037	0.9696	0.4021	-0.4274	0.2115	0.0063	0.0421	0.0145	0.15	0.2081	-39.9815	-9.2734	71.2506
16	5.4988	-0.9163	0.4271	0.8333	-0.2873	0.1018	0.1122	-0.1514	-0.1994	0.0182	-0.107	-0.0489	0.0179	-0.0168	-0.0052	-0.0056	-0.036	0.0552	-0.1081	0.0414	0.0002	-52.4658	-1.0383	64.7709
17	21.8062	2.4285	1.5956	0.2704	0.1777	0.1168	0.7342	-0.0207	-2.4348	-0.3728	1.0809	2.085	1.0347	-0.9489	-1.8151	0.9786	-0.0334	0.0157	0.7255	0.324	0.7883	-81.8725	-4.109	65.2439
18	3.6149	-0.125	-0.8338	1.5481	0.8508	2.5585	0.0193	0.01	0.1533	0.1293	0.0217	0.1486	0.0489	-0.3611	-0.041	0.0294	-0.0834	0.0388	-0.0053	0.0543	0.0439	-74.4391	-1.287	74.9125
19	10.3938	-1.9403	-3.8717	2.1747	0.2141	5.2901	0.0076	-0.3627	-0.6762	-0.0106	-0.0851	-0.2013	0.3476	0.0656	0.0775	0.0763	-0.1492	-0.0202	-0.0561	0.1447	0.1614	-71.5733	-8.2479	80.2601
20	16.3966	-3.7395	1.6835	8.5106	-1.6071	4.355	-0.0436	-0.6531	-0.3349	0.1788	-0.1673	0.2448	0.3984	-0.3169	0.2109	0.0686	-0.1726	-0.0103	0.033	0.0613	0.0439	-82.3574	-12.89	83.9639

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	5 - 63	25 - 83
2	X-RAY DIFFRACTION	2	A	A	64 - 78	84 - 98
3	X-RAY DIFFRACTION	3	A	A	79 - 115	99 - 135
4	X-RAY DIFFRACTION	4	A	A	116 - 207	136 - 227
5	X-RAY DIFFRACTION	5	A	A	208 - 241	228 - 261
6	X-RAY DIFFRACTION	6	A	A	242 - 301	262 - 321
7	X-RAY DIFFRACTION	7	A	A	302 - 318	322 - 338
8	X-RAY DIFFRACTION	8	A	A	319 - 361	339 - 381
9	X-RAY DIFFRACTION	9	A	A	362 - 394	382 - 414
10	X-RAY DIFFRACTION	10	A	A	395 - 436	415 - 456
11	X-RAY DIFFRACTION	11	B	B	5 - 63	25 - 83
12	X-RAY DIFFRACTION	12	B	B	64 - 78	84 - 98
13	X-RAY DIFFRACTION	13	B	B	79 - 115	99 - 135
14	X-RAY DIFFRACTION	14	B	B	116 - 207	136 - 227
15	X-RAY DIFFRACTION	15	B	B	208 - 241	228 - 261
16	X-RAY DIFFRACTION	16	B	B	242 - 301	262 - 321
17	X-RAY DIFFRACTION	17	B	B	302 - 318	322 - 338
18	X-RAY DIFFRACTION	18	B	B	319 - 361	339 - 381
19	X-RAY DIFFRACTION	19	B	B	362 - 394	382 - 414
20	X-RAY DIFFRACTION	20	B	B	395 - 436	415 - 456

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