PDB-2wxb: Acetylglutamate kinase from Escherichia coli free of substrates

ID or keywords:

Entry

Database: PDB / ID: 2wxb

Title

Acetylglutamate kinase from Escherichia coli free of substrates

Components

ACETYLGLUTAMATE KINASE

Keywords

TRANSFERASE / ACETYLGLUTAMATE KINASE / AMINOACID KINASE FAMILY / KINASE / ARGININE BIOSYNTHESIS

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

Ramon-Maiques, S. / 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	Nov 6, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 12, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jul 24, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4	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_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_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	2wxb.cif.gz	112.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2wxb.ent.gz	88.8 KB	Display	PDB format
PDBx/mmJSON format	2wxb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2wxb_validation.pdf.gz	474.6 KB	Display	wwPDB validaton report
Full document	2wxb_full_validation.pdf.gz	482.5 KB	Display
Data in XML	2wxb_validation.xml.gz	22.4 KB	Display
Data in CIF	2wxb_validation.cif.gz	31.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wx/2wxb ftp://data.pdbj.org/pub/pdb/validation_reports/wx/2wxb	HTTPS FTP

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Related structure data

Related structure data	2x2wC 1gs5S 1gsj 1oh9 1oha 1ohb S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2x2w-d 3t7b-d 5bro-d 3vgf-d 6awi-2 20807 3vgh-d 6bzg-d 4jz7-1 6awj-2 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	#127 - Jul 2010 Crystallins similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: ACETYLGLUTAMATE KINASE

B: ACETYLGLUTAMATE KINASE

hetero molecules

54.8 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)	78.696, 78.696, 277.743
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:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	1 - 54
2	1	1	5	B	1 - 54
1	2	1	5	A	73 - 178
2	2	1	5	B	73 - 178

NCS oper: (Code: given
Matrix: (0.2369, 0.8983, 0.3702), (0.8866, -0.3557, 0.2956), (0.3972, 0.2581, -0.8807)
Vector: -74.11, 31.1, 165.6)

#1: Protein	ACETYLGLUTAMATE KINASE / NAG KINASE / AGK / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / N-ACETYL-L-GLUTAMATE KINASE 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-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₂S₂
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 176 / 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	pH: 5.6 Details: 0.1 M SODIUM CITRATE PH 5.6, 26-32% PEG 4000 AND 0.1-0.3 M AMMONIUM ACETATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8468
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 24, 1999
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8468 Å / Relative weight: 1
Reflection	Resolution: 1.95→20 Å / Num. obs: 35514 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6 % / R_merge(I) obs: 0.05 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2→2.11 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.28 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0072	refinement
MOSFLM		data reduction
SCALA		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GS5

1gs5

Resolution: 2→19.95 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.939 / SU B: 10.213 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.247	1761	5 %	RANDOM
R_work	0.214	-	-	-
obs	0.216	33717	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: 42.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.44 Å²	-0.72 Å²	0 Å²
2-	-	-1.44 Å²	0 Å²
3-	-	-	2.16 Å²

Refinement step

Cycle: LAST / Resolution: 2→19.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3796	0	24	176	3996

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	3862
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2535
X-RAY DIFFRACTION	r_angle_refined_deg	1.203	1.996	5233
X-RAY DIFFRACTION	r_angle_other_deg	0.838	3	6280
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.786	5	513
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.011	25.775	142
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.823	15	679
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.809	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	639
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	4287
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	651
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	0.482	1.5	2544
X-RAY DIFFRACTION	r_mcbond_other	0.135	1.5	1062
X-RAY DIFFRACTION	r_mcangle_it	0.836	2	4057
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.477	3	1318
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.33	4.5	1176
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	930	medium positional	0.35	0.5
2	B	930	medium positional	0.35	0.5
1	A	972	loose positional	0.72	5
2	B	972	loose positional	0.72	5
1	A	930	medium thermal	0.53	2
2	B	930	medium thermal	0.53	2
1	A	972	loose thermal	0.62	10
2	B	972	loose thermal	0.62	10

LS refinement shell

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

	R_factor	Num. reflection	% reflection
R_free	0.28	130	-
R_work	0.237	2401	-
obs	-	-	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	5.4835	1.0454	2.0451	4.6468	-0.0564	4.9017	0.2603	-0.5605	-0.3286	0.5472	-0.1763	0.066	0.2006	0.0128	-0.0839	0.2011	-0.0062	0.0649	0.237	0.0459	0.0718	9.378	57.86	116.153
2	11.5906	3.7831	1.1229	1.9019	1.0004	0.7236	0.3321	-0.9143	0.6873	0.133	-0.0717	-0.097	-0.0066	0.1368	-0.2603	0.2974	-0.0339	0.0242	0.3408	-0.0686	0.2545	25.309	69.665	109.007
3	13.2958	-7.1076	1.1427	3.8703	-0.7655	0.5636	-0.2182	-0.4573	0.865	0.0593	0.1798	-0.4691	-0.051	-0.0067	0.0385	0.4043	-0.0218	-0.0146	0.3523	-0.0603	0.3701	25.169	82.578	103.935
4	3.0878	0.4761	0.5997	4.5769	-0.9673	2.6463	-0.0536	-0.1935	-0.0879	0.1012	-0.0335	-0.168	-0.1084	0.1472	0.0871	0.0574	0.0179	0.0163	0.0929	0.0018	0.0233	19.17	62.298	103.484
5	4.2287	0.7001	-0.7374	3.628	-0.1112	1.6483	-0.0588	0.0726	0.1149	-0.2496	0.0767	0.3188	-0.1469	-0.0361	-0.018	0.0658	0.0097	-0.0232	0.0715	0.0031	0.029	10.484	66.706	99.013
6	5.9972	-6.6158	-1.0094	7.8459	2.2899	6.6611	-0.7563	-1.3127	0.5907	0.8637	0.9483	-0.4613	-0.2456	-0.0319	-0.192	0.3149	0.0044	0.0472	0.8896	-0.2566	0.3128	2.111	74.441	123.609
7	10.5117	1.4513	-2.7323	1.0085	1.9767	13.2277	-0.7365	-0.5205	1.0988	0.0074	0.5372	-0.0824	-0.9758	0.6042	0.1993	0.992	0.2178	-0.3806	0.8147	-0.3503	0.628	4.495	84.08	120.888
8	2.6321	-1.819	1.0866	6.0505	-1.9697	5.4267	-0.0917	-0.4766	-0.0265	0.5083	-0.0069	-0.0196	0.2038	0.1134	0.0987	0.2239	0.0088	0.0398	0.2732	-0.0276	0.1288	2.172	68.578	117.368
9	2.4613	-0.2671	0.3843	5.604	-0.7512	3.0086	-0.1282	0.216	-0.0173	-0.4516	0.0562	-0.2071	-0.3629	0.1537	0.072	0.2454	-0.0161	0.0635	0.1447	-0.0242	0.0687	23.369	52.673	82.745
10	8.7247	10.9271	5.9692	13.7341	7.5127	4.1202	-0.311	0.3507	-0.2641	-0.3081	0.5061	-0.3677	-0.1668	0.3376	-0.1952	0.2057	0.0197	0.04	0.3296	0.0099	0.2902	34.104	60.233	96.993
11	6.1945	-4.5851	1.2996	14.2565	-6.2595	2.9315	-0.2445	0.0434	-0.1389	-0.9243	-0.0272	-1.1638	0.5371	0.0709	0.2716	0.3818	0.0535	-0.021	0.5464	-0.1807	1.1511	43.471	54.726	105.61
12	2.7907	0.4878	0.5671	3.2564	0.2806	1.9959	-0.0432	-0.2314	-0.3558	0.1131	0.0948	-0.3279	0.0756	0.164	-0.0515	0.0818	0.0176	0.0552	0.104	0.0107	0.1171	24.895	52.381	99.887
13	1.6215	-0.5179	-0.0669	2.2844	0.7163	2.583	-0.019	-0.1497	-0.2516	0.0977	0.1198	-0.0879	0.1446	0.1846	-0.1008	0.0933	0.0078	0.0394	0.0865	0.0342	0.1477	25.005	46.968	97.286
14	4.0687	-4.5838	-2.016	8.28	2.508	1.3157	0.2257	-0.0193	0.1172	-0.2294	0.0145	-0.4256	-0.064	0.3351	-0.2402	0.4619	-0.0721	0.1305	0.4569	-0.0883	0.3689	41.966	41.191	77.208
15	9.5398	4.0713	-2.0163	2.9874	2.8682	11.6819	-0.1066	-0.2203	-0.4788	-0.2331	0.4968	-0.4661	-0.4381	1.956	-0.3902	0.5207	0.0522	0.0557	0.6905	0.0536	0.9008	47.246	39.742	85.637
16	4.9345	-0.1602	0.1951	6.3289	-0.3516	3.8388	-0.0582	0.1815	0.2925	-0.4835	0.079	-0.5503	-0.2081	0.2564	-0.0207	0.2023	-0.0222	0.1086	0.1881	-0.0658	0.2411	32.502	43.071	81.966

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 39
2	X-RAY DIFFRACTION	2	A	40 - 55
3	X-RAY DIFFRACTION	3	A	56 - 66
4	X-RAY DIFFRACTION	4	A	67 - 113
5	X-RAY DIFFRACTION	5	A	114 - 176
6	X-RAY DIFFRACTION	6	A	177 - 199
7	X-RAY DIFFRACTION	7	A	200 - 217
8	X-RAY DIFFRACTION	8	A	218 - 258
9	X-RAY DIFFRACTION	9	B	1 - 38
10	X-RAY DIFFRACTION	10	B	39 - 55
11	X-RAY DIFFRACTION	11	B	56 - 69
12	X-RAY DIFFRACTION	12	B	70 - 137
13	X-RAY DIFFRACTION	13	B	138 - 179
14	X-RAY DIFFRACTION	14	B	180 - 199
15	X-RAY DIFFRACTION	15	B	200 - 217
16	X-RAY DIFFRACTION	16	B	218 - 258

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