PDB-2x2w: Acetylglutamate kinase from Escherichia coli bound to N-acetyl-L-...

ID or keywords:

Entry

Database: PDB / ID: 2x2w

Title

Acetylglutamate kinase from Escherichia coli bound to N-acetyl-L-glutamyl-5-phosphate

Components

ACETYLGLUTAMATE KINASE

Keywords

TRANSFERASE / ARGININE BIOSYNTHESIS / ATP-BINDING / NUCLEOTIDE-BINDING / AMINO-ACID BIOSYNTHESIS / AMINO ACID KINASE FAMILY

Function / homology

Function and homology information

acetylglutamate kinase / acetylglutamate kinase activity / L-arginine biosynthetic process via ornithine / L-arginine biosynthetic process / DNA damage response / ATP binding / cytoplasm
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Gil-Ortiz, F. / Rubio, V.

Citation

Journal: J. Mol. Biol. / Year: 2010
Title: Two crystal structures of Escherichia coli N-acetyl-L-glutamate kinase demonstrate the cycling between open and closed conformations.
Authors: Gil-Ortiz, F. / Ramon-Maiques, S. / Fernandez-Murga, M.L. / Fita, I. / Rubio, V.

History

Deposition	Jan 18, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2013	Group: Refinement description
Revision 1.2	Mar 6, 2019	Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / reflns_shell / struct_biol Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _reflns_shell.pdbx_Rsym_value
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_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_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2x2w.cif.gz	113.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2x2w.ent.gz	89.8 KB	Display	PDB format
PDBx/mmJSON format	2x2w.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2x2w_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	2x2w_full_validation.pdf.gz	1 MB	Display
Data in XML	2x2w_validation.xml.gz	22.2 KB	Display
Data in CIF	2x2w_validation.cif.gz	30.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x2/2x2w ftp://data.pdbj.org/pub/pdb/validation_reports/x2/2x2w	HTTPS FTP

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Related structure data

Related structure data	2wxbSC 1gs5 1gsj 1oh9 1oha 1ohb S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2wxb-d 3t7b-d 5bro-d 6awi-2 6a4b-3 20807 3vgf-d 3f9k-1 1ey2-d 6f2g-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

Deposited unit

A: ACETYLGLUTAMATE KINASE

B: ACETYLGLUTAMATE KINASE

hetero molecules

55.1 kDa, 2 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)	78.652, 78.652, 283.054
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	MET	MET	GLY	GLY	A	A	1 - 54	1 - 54
2	1	MET	MET	GLY	GLY	B	B	1 - 54	1 - 54
1	2	ILE	ILE	LEU	LEU	A	A	73 - 178	73 - 178
2	2	ILE	ILE	LEU	LEU	B	B	73 - 178	73 - 178

NCS oper: (Code: given
Matrix: (0.236, 0.8912, 0.3873), (0.8841, -0.3623, 0.2951), (0.4033, 0.2728, -0.8734)
Vector: -75.6, 30.51, 167.6)

#1: Protein	ACETYLGLUTAMATE KINASE / N-ACETYL-L-GLUTAMATE KINASE / NAG KINASE / AGK / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE Mass: 27186.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Plasmid: PET15-B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A6C8, UniProt: A0A140NEG9*PLUS, acetylglutamate kinase
#2: Chemical	ChemComp-X2W / N-ACETYL-L-GLUTAMYL 5-PHOSPHATE / N-ACETYL-5-OXO-5-(PHOSPHONOOXY)-L-NORVALINE Type: L-peptide linking / Mass: 269.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₂NO₈P
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.3 Å³/Da / Density % sol: 46 % / Description: NONE
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30-35 % PEG MONOMETHYL ETHER 5K, 0.1 M MES PH 6.5, 0.1-0.2 M (NH4)2SO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2001
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2→29.24 Å / Num. obs: 35550 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 12.6 % / R_sym value: 0.071 / Net I/σ(I): 44
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 6.3 / R_sym value: 0.406 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0072	refinement
HKL-2000		data reduction
HKL-2000	K	data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WXB

2wxb

Resolution: 2→20 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.939 / SU B: 8.35 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.225	1802	5 %	RANDOM
R_work	0.199	-	-	-
obs	0.2	34319	99.9 %	-

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: 39.1 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.51 Å²	-0.25 Å²	0 Å²
2-	-	-0.51 Å²	0 Å²
3-	-	-	0.76 Å²

Refinement step

Cycle: LAST / Resolution: 2→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3808	0	44	157	4009

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	3894
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2544
X-RAY DIFFRACTION	r_angle_refined_deg	1.168	2.001	5282
X-RAY DIFFRACTION	r_angle_other_deg	0.838	3.001	6286
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.736	5	514
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.546	25.775	142
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.949	15	686
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.438	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	640
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	4316
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	654
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	0.411	1.5	2556
X-RAY DIFFRACTION	r_mcbond_other	0.108	1.5	1066
X-RAY DIFFRACTION	r_mcangle_it	0.764	2	4078
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.359	3	1338
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.235	4.5	1204
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	936	medium positional	0.4	0.5
2	B	936	medium positional	0.4	0.5
1	A	992	loose positional	0.75	5
2	B	992	loose positional	0.75	5
1	A	936	medium thermal	0.55	2
2	B	936	medium thermal	0.55	2
1	A	992	loose thermal	0.55	10
2	B	992	loose thermal	0.55	10

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.254	121	-
R_work	0.216	2442	-
obs	-	-	99.81 %

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	12.9341	2.8787	5.0536	7.0739	2.2339	7.7776	0.3096	-0.5117	-0.0804	0.555	-0.1688	0.0836	0.1038	-0.0057	-0.1408	0.1436	0.0633	0.0505	0.1172	0.0212	0.0325	5.622	61.796	113.433
2	10.8389	4.2611	-0.1569	9.7126	0.2616	4.5874	0.1174	-0.7178	0.2461	0.6946	-0.0851	-0.2837	-0.4324	0.325	-0.0322	0.2865	0.0064	0.0072	0.3127	0.009	0.1444	15.741	58.362	122.174
3	9.1844	-1.4634	-4.8571	0.9243	0.212	4.019	0.1113	-1.2221	-0.1083	0.4407	-0.0455	0.115	-0.1396	0.6135	-0.0658	0.4034	-0.2046	0.054	0.4272	0.013	0.0258	12.162	59.698	113.938
4	0.6402	-2.9201	0.7667	13.4487	-3.5624	1.1072	0.0928	-0.0733	0.0943	-0.5889	0.144	-0.1062	0.0033	-0.2807	-0.2367	0.6796	0.1367	0.0714	0.9029	-0.1866	1.0187	27.687	79.95	107.049
5	3.2315	-0.4708	-0.2208	2.7085	-0.4018	2.2002	-0.0027	-0.0731	0.2193	-0.017	0.0317	-0.0475	-0.1414	0.1128	-0.0291	0.0204	-0.0038	0.0129	0.0552	-0.0206	0.0364	14.075	64.758	103.675
6	6.3762	-6.4415	-9.6888	6.7382	10.5954	17.5993	-0.6599	-0.4245	-0.2045	0.3553	0.2584	0.2323	-0.1608	0.2286	0.4014	0.6114	-0.0015	-0.0106	0.6538	-0.075	0.626	3.047	76.65	130.157
7	4.0813	-0.239	0.074	8.0215	-8.062	11.4697	-0.2584	-0.6911	-0.0225	0.6954	-0.0178	-0.2502	-0.3312	-0.0113	0.2761	0.3312	0.047	0.0398	0.368	-0.0504	0.2717	-3.122	76.273	124.914
8	13.8041	5.4064	-1.1332	7.069	2.0958	10.5085	-0.4433	-0.3817	0.8383	0.6277	0.3139	-0.1892	-0.8522	-0.0059	0.1293	0.94	0.143	-0.2787	0.5341	-0.2228	0.4019	4.929	84.169	122.92
9	8.5865	-1.1373	5.1157	0.4551	0.5029	12.1054	-0.1016	-0.113	0.468	0.0595	0.0242	-0.0622	-0.2107	0.3315	0.0773	0.1637	-0.0119	0.0115	0.1146	-0.0054	0.1304	0.905	75.709	111.38
10	1.897	-2.9463	1.6743	10.8175	-1.6443	3.823	-0.2605	-0.5457	-0.2052	1.2364	0.3218	-0.0728	0.235	0.1379	-0.0612	0.3192	0.0759	0.0707	0.4825	0.061	0.1999	2.811	65.721	122.667
11	2.2117	-0.8203	0.3048	5.5851	0.3451	3.7125	0.0209	-0.0545	0.3833	-0.0797	0.0095	-0.3448	-0.4864	0.2962	-0.0305	0.1137	-0.0079	0.0555	0.0512	0.0114	0.1107	27.324	51.936	88.363
12	2.2376	-0.2452	0.7504	4.7124	-0.2212	2.7584	-0.0331	0.2676	0.134	-0.6989	0.0651	0.014	-0.1741	0.0093	-0.032	0.1598	-0.008	0.0536	0.073	0.0255	0.0833	21.972	52.826	83.262
13	8.058	5.4942	3.4439	11.9246	7.5018	5.6832	-0.2789	0.4852	-0.1514	-0.141	0.1228	-0.2404	0.2886	0.5134	0.156	0.2385	0.0844	0.073	0.3743	0.0598	0.2992	38.048	63.365	101.242
14	1.6019	3.3411	0.724	12.2167	-0.5337	1.128	0.0794	0.3115	-0.4199	-0.3096	0.0371	-1.1546	0.2469	0.3881	-0.1166	0.3988	0.0292	0.0633	0.5909	-0.0102	0.4908	43.917	55.945	105.975
15	2.257	0.2816	0.3873	3.5684	0.1781	2.4932	0.0225	-0.2805	-0.0882	0.2008	0.0361	-0.3992	0.1227	0.2456	-0.0585	0.04	0.019	0.0097	0.1301	0.0103	0.0949	26.593	52.524	102.615
16	1.8953	0.0379	0.4961	2.2527	0.9022	3.6021	-0.0687	-0.2517	-0.1658	0.1407	0.1659	-0.0139	0.1901	0.0751	-0.0973	0.0386	0.0249	0.034	0.061	0.0305	0.0694	23.354	46.485	99.186
17	3.491	-0.9336	-2.2218	2.7967	1.7687	3.5813	0.1507	0.1023	0.0168	-0.3973	0.0171	-0.7609	0.1934	0.1562	-0.1678	0.2792	-0.0352	0.1366	0.1742	-0.0174	0.3182	41.706	41.376	78.942
18	10.5605	-3.8399	0.2364	7.4112	2.9454	7.4881	0.2743	0.6532	-0.1521	0.2433	-0.031	-0.9702	0.4122	0.9399	-0.2432	0.2812	-0.0092	-0.0027	0.3854	-0.0692	0.4547	47.768	39.152	86.721
19	5.255	1.9331	-0.5369	8.1323	-0.1941	2.6683	-0.0511	-0.0984	0.0277	-0.1684	0.1848	-0.454	-0.0642	0.1346	-0.1338	0.0508	0.0067	0.0811	0.1147	-0.0533	0.1685	34.686	42.208	87.569
20	7.5697	-5.2755	5.1576	9.2922	-0.2755	8.5582	-0.0087	0.2528	0.1228	-1.1477	0.0129	-0.1509	-0.4459	-0.0152	-0.0042	0.3191	-0.0561	0.1198	0.0891	0.0027	0.2011	30.172	44.05	78.654

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 12
2	X-RAY DIFFRACTION	2	A	13 - 29
3	X-RAY DIFFRACTION	3	A	30 - 51
4	X-RAY DIFFRACTION	4	A	52 - 66
5	X-RAY DIFFRACTION	5	A	67 - 181
6	X-RAY DIFFRACTION	6	A	182 - 190
7	X-RAY DIFFRACTION	7	A	191 - 200
8	X-RAY DIFFRACTION	8	A	201 - 217
9	X-RAY DIFFRACTION	9	A	218 - 230
10	X-RAY DIFFRACTION	10	A	231 - 258
11	X-RAY DIFFRACTION	11	B	1 - 18
12	X-RAY DIFFRACTION	12	B	19 - 43
13	X-RAY DIFFRACTION	13	B	44 - 55
14	X-RAY DIFFRACTION	14	B	56 - 66
15	X-RAY DIFFRACTION	15	B	67 - 132
16	X-RAY DIFFRACTION	16	B	133 - 177
17	X-RAY DIFFRACTION	17	B	178 - 199
18	X-RAY DIFFRACTION	18	B	200 - 217
19	X-RAY DIFFRACTION	19	B	218 - 240
20	X-RAY DIFFRACTION	20	B	241 - 258

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