PDB-6mx1: The crystal structure of the regulatory domain of aspartokinase i...

ID or keywords:

Entry

Database: PDB / ID: 6mx1

Title

The crystal structure of the regulatory domain of aspartokinase in the bifunctional aspartokinase/homoserine dehydrogenase 1 from Escherichia coli str. K-12 substr. MG1655

Components

Bifunctional aspartokinase/homoserine dehydrogenase 1

Keywords

TRANSFERASE / HYDROLASE / bifunctional aspartokinase/homoserine dehydrogenase 1 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

aspartate kinase / aspartate kinase activity / homoserine dehydrogenase / homoserine dehydrogenase activity / homoserine biosynthetic process / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / NADP binding / ATP binding
Similarity search - Function

Biological species

Escherichia coli str. K-12 substr. MG1655 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.671 Å

Authors

Tan, K. / Endres, M. / Welk, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The crystal structure of the regulatory domain of aspartokinase in the bifunctional aspartokinase/homoserine dehydrogenase 1 from Escherichia coli str. K-12 substr. MG1655
Authors: Tan, K. / Endres, M. / Welk, L. / Joachimiak, A.

History

Deposition	Oct 30, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 7, 2018	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6mx1.cif.gz	132.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6mx1.ent.gz	103.9 KB	Display	PDB format
PDBx/mmJSON format	6mx1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6mx1_validation.pdf.gz	437.2 KB	Display	wwPDB validaton report
Full document	6mx1_full_validation.pdf.gz	439.7 KB	Display
Data in XML	6mx1_validation.xml.gz	13.5 KB	Display
Data in CIF	6mx1_validation.cif.gz	18.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mx/6mx1 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/6mx1	HTTPS FTP

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Related structure data

Related structure data	3c1nS S: Starting model for refinement
Similar structure data	1bt1-2 4acy-2 1f76-3 7cyk-1 4aks-2 1bt3-d 3azt-2 5ylk-2 1v93-d 4ad3-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP96086 TargetTrack: IDP96086

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#61 - Jan 2005 Phenylalanine Hydroxylase similarity (3) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (3)

Deposited unit

A: Bifunctional aspartokinase/homoserine dehydrogenase 1

B: Bifunctional aspartokinase/homoserine dehydrogenase 1

35 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)	92.642, 54.550, 65.242
Angle α, β, γ (deg.)	90.00, 99.30, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Bifunctional aspartokinase/homoserine dehydrogenase 1 / Aspartokinase I/homoserine dehydrogenase I / AKI-HDI Mass: 17523.170 Da / Num. of mol.: 2 / Fragment: regulatory domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: thrA, thrA1, thrA2, b0002, JW0001 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3)magic (bacteria) / Strain (production host): BL21(DE3)magic References: UniProt: P00561, aspartate kinase, homoserine dehydrogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Bifunctional aspartokinase/homoserine dehydrogenase 1 / Aspartokinase I/homoserine dehydrogenase I / AKI-HDI

Mass: 17523.170 Da / Num. of mol.: 2 / Fragment: regulatory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: thrA, thrA1, thrA2, b0002, JW0001 / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3)magic (bacteria) / Strain (production host): BL21(DE3)magic
References: UniProt: P00561, aspartate kinase, homoserine dehydrogenase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.25 Å³/Da / Density % sol: 45.24 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Bis-Tris Propane:NaCl, 2.8 M Sodium Acetate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 13, 2018 / Details: Mirror
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 1.67→50 Å / Num. obs: 36373 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / B_iso Wilson estimate: 28.645 Å² / R_merge(I) obs: 0.072 / R_pim(I) all: 0.043 / R_rim(I) all: 0.084 / Χ²: 1.303 / Net I/σ(I): 26.6
Reflection shell	Resolution: 1.67→1.71 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.715 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 1678 / CC_1/2: 0.59 / R_pim(I) all: 0.47 / R_rim(I) all: 0.86 / Χ²: 0.72 / % possible all: 91.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3C1N

3c1n

Resolution: 1.671→46.845 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.61

	R_factor	Num. reflection	% reflection
R_free	0.2155	1858	5.11 %
R_work	0.1781	-	-
obs	0.18	36356	97.36 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.671→46.845 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2278	0	0	93	2371

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	2319
X-RAY DIFFRACTION	f_angle_d	1.291	3134
X-RAY DIFFRACTION	f_dihedral_angle_d	6.531	1915
X-RAY DIFFRACTION	f_chiral_restr	0.088	379
X-RAY DIFFRACTION	f_plane_restr	0.008	405

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 (%)
1.6711-1.7162	0.2948	138	0.274	2301	X-RAY DIFFRACTION	86
1.7162-1.7667	0.2794	138	0.2484	2608	X-RAY DIFFRACTION	96
1.7667-1.8238	0.2764	161	0.2386	2564	X-RAY DIFFRACTION	96
1.8238-1.889	0.2757	137	0.2153	2683	X-RAY DIFFRACTION	99
1.889-1.9646	0.2359	155	0.1976	2701	X-RAY DIFFRACTION	99
1.9646-2.054	0.2476	138	0.1911	2662	X-RAY DIFFRACTION	99
2.054-2.1623	0.2462	133	0.1842	2673	X-RAY DIFFRACTION	98
2.1623-2.2978	0.232	156	0.1843	2658	X-RAY DIFFRACTION	98
2.2978-2.4752	0.2049	127	0.1925	2731	X-RAY DIFFRACTION	99
2.4752-2.7242	0.251	143	0.1951	2708	X-RAY DIFFRACTION	99
2.7242-3.1184	0.2255	144	0.1897	2710	X-RAY DIFFRACTION	99
3.1184-3.9285	0.212	148	0.1754	2718	X-RAY DIFFRACTION	99
3.9285-46.8632	0.173	140	0.1472	2781	X-RAY DIFFRACTION	99

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	2.0319	2.2397	3.8784	4.5114	3.1726	7.9673	0.1257	0.2678	0.0956	0.1065	0.0046	-0.0524	-0.1508	0.0986	-0.1742	0.2321	0.0584	0.0427	0.2435	-0.0055	0.2388	5.7237	28.927	60.1042
2	1.9567	2.6325	-2.6138	4.6122	-4.624	4.5994	-0.5623	1.2545	0.1555	-1.1121	0.4872	0.7389	0.213	-0.513	0.0303	0.6362	-0.1612	-0.0568	0.7072	0.0362	0.3684	-0.6297	19.5437	36.3145
3	3.3523	0.6099	-3.4964	4.8574	4.8224	9.7882	-0.2971	-0.5004	-0.2873	-0.4595	0.3226	0.206	-0.2247	0.1701	0.036	0.377	0.177	0.0054	0.4131	0.1606	0.3529	-4.5939	31.5365	42.4104
4	3.6913	0.9624	1.4333	3.451	-1.8774	5.8702	-0.1986	0.1811	-0.4329	-0.1251	0.2175	0.4033	-0.023	-0.1761	-0.0556	0.2639	0.0102	-0.0307	0.3085	0.0289	0.3199	2.3102	26.2783	47.1932
5	7.8752	0.0549	0.2004	0.8251	2.1036	5.6574	0.0516	0.1005	0.355	-0.1042	-0.1589	0.1759	-0.2882	-0.5552	0.0524	0.3183	0.1056	0.0082	0.349	0.0412	0.3232	-8.3056	28.1519	51.0245
6	4.3442	4.011	-2.6933	5.3179	-2.7587	1.7339	-0.7987	0.3009	-0.4415	-1.7897	0.6633	0.8983	0.2866	-1.5822	0.2127	0.5617	-0.0162	-0.1362	0.7684	0.0338	0.3686	-12.9042	20.4158	38.1098
7	6.4644	3.5082	4.2161	8.1418	5.2532	4.605	0.8282	-0.3658	-0.2995	0.3863	-0.0589	-0.1195	1.223	-1.692	-0.3424	0.2429	-0.0027	-0.005	0.349	0.0322	0.2487	-6.5319	18.5419	49.7809
8	4.5593	-2.8441	2.2222	5.6888	0.8505	6.325	0.0458	0.092	0.2597	-0.0234	0.1177	-0.7843	-0.0396	0.6384	-0.1564	0.2102	-0.0119	0.03	0.2	-0.004	0.2619	15.3437	23.6712	60.8343
9	4.1873	-0.2159	0.8394	3.5025	1.5942	8.4794	0.1077	-0.1994	0.1681	0.045	0.0721	-0.204	-0.1575	0.1863	-0.1437	0.2259	0.0124	-0.0162	0.1014	-0.0214	0.2345	11.9897	25.8369	64.4416
10	4.1473	-0.1371	-0.5899	4.9733	-2.8291	3.8517	0.3669	0.3563	0.7508	0.3183	-0.4203	-0.2668	-0.7238	0.3024	0.1792	0.4169	0.004	0.0973	0.2726	0.0678	0.4499	18.1726	29.2392	41.5314
11	0.9231	0.3335	1.3198	3.626	-0.8045	4.1425	0.0192	0.0404	-0.0082	0.098	0.0135	0.0307	0.1198	-0.101	-0.0259	0.2613	0.0729	0.0204	0.2658	0.0115	0.3043	17.3315	12.5508	54.9251
12	2.4559	-4.0106	0.647	6.437	-2.2323	5.9816	-0.0987	0.077	0.1608	-0.0097	-0.0777	-0.0069	0.0903	0.0104	0.1146	0.2461	0.0319	0.0315	0.1822	0.007	0.1835	15.3492	19.8573	50.4449
13	2.0758	1.2713	-2.6344	3.631	-4.2493	7.044	0.266	0.0385	0.1095	-0.2282	-0.5337	-0.5894	0.1021	0.6519	0.4222	0.2716	0.0246	0.0299	0.3201	0.0277	0.3762	25.2037	16.5909	45.8628
14	9.6895	5.012	3.2755	7.1206	-0.9581	2.6837	0.5098	0.1521	-0.5135	0.1805	-0.5122	-0.2698	0.3322	0.1782	0.0295	0.3533	0.0854	-0.0114	0.2679	0.0095	0.2771	20.9572	2.3823	50.921
15	1.6779	0.2925	-0.6248	6.8265	-2.3512	3.0884	0.2053	0.1984	0.3786	-0.3847	-0.265	-0.4348	-0.331	0.0014	0.1389	0.3162	0.0115	0.0128	0.2454	0.0081	0.2552	14.8927	23.8047	43.3489
16	5.9883	0.7362	0.8417	4.3053	-3.693	3.7661	0.2878	0.2216	0.7301	-0.0005	-0.0818	0.6716	-0.5134	-0.7017	-0.3003	0.4623	0.1271	0.105	0.4334	0.0677	0.3797	4.1415	34.3006	38.2409
17	2.8324	0.245	0.0434	5.8292	-3.934	3.1466	0.4869	0.4249	0.7103	-0.0449	-0.0399	-0.2235	-1.3517	-0.2062	-0.184	0.5989	0.0881	0.1601	0.2747	0.1057	0.3655	11.1239	35.1081	39.0119

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 305 through 320 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 321 through 330 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 331 through 341 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 342 through 357 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 358 through 377 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 378 through 384 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 385 through 395 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 396 through 431 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 432 through 460 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 306 through 320 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 321 through 341 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 342 through 357 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 358 through 377 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 378 through 384 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 385 through 407 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 408 through 428 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 429 through 460 )

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