PDB-3c1n: Crystal Structure of Allosteric Inhibition Threonine-sensitive As...

ID or keywords:

Entry

Database: PDB / ID: 3c1n

Title

Crystal Structure of Allosteric Inhibition Threonine-sensitive Aspartokinase from Methanococcus jannaschii with L-threonine

Components

Probable aspartokinase

Keywords

TRANSFERASE / kinase / allosteric inhibition / threonine-sensitive / ACT domain / Amino-acid biosynthesis / Threonine biosynthesis

Function / homology

Function and homology information

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

Biological species

Methanocaldococcus jannaschii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.72 Å

Authors

Liu, X. / Pavlovshy, A.G. / Viola, R.E.

Citation

Journal: J.Biol.Chem. / Year: 2008
Title: The Structural Basis for Allosteric Inhibition of a Threonine-sensitive Aspartokinase.
Authors: Liu, X. / Pavlovsky, A.G. / Viola, R.E.

History

Deposition	Jan 23, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 25, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.3	Aug 30, 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_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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	3c1n.cif.gz	338.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3c1n.ent.gz	276.8 KB	Display	PDB format
PDBx/mmJSON format	3c1n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3c1n_validation.pdf.gz	485.6 KB	Display	wwPDB validaton report
Full document	3c1n_full_validation.pdf.gz	524 KB	Display
Data in XML	3c1n_validation.xml.gz	63.4 KB	Display
Data in CIF	3c1n_validation.cif.gz	85.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c1/3c1n ftp://data.pdbj.org/pub/pdb/validation_reports/c1/3c1n	HTTPS FTP

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Related structure data

Related structure data	3c1mSC 3c20C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5d8q-d 4pph-d 5r1r-7 4cmr-1 5r1r-8 3bkn-d Search similar-shape structures by Omokage search (details) 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	#61 - Jan 2005 Phenylalanine Hydroxylase similarity (3) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (3)

Deposited unit

A: Probable aspartokinase

B: Probable aspartokinase

C: Probable aspartokinase

D: Probable aspartokinase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

2

A: Probable aspartokinase

B: Probable aspartokinase

hetero molecules

defined by author&software
103 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Probable aspartokinase

D: Probable aspartokinase

hetero molecules

defined by author&software
103 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	110.039, 144.317, 155.358
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-ID	Ens-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	THR	THR	GLY	GLY	B	B	3 - 165	3 - 165
2	1	THR	THR	GLY	GLY	A	A	3 - 165	3 - 165
3	1	THR	THR	GLY	GLY	C	C	3 - 165	3 - 165
4	1	THR	THR	GLY	GLY	D	D	3 - 165	3 - 165
1	2	LYS	LYS	GLU	GLU	B	B	170 - 290	170 - 290
2	2	LYS	LYS	GLU	GLU	A	A	170 - 290	170 - 290
3	2	LYS	LYS	GLU	GLU	C	C	170 - 290	170 - 290
4	2	LYS	LYS	GLU	GLU	D	D	170 - 290	170 - 290
1	3	ASN	ASN	ASP	ASP	B	B	300 - 383	300 - 383
2	3	ASN	ASN	ASP	ASP	A	A	300 - 383	300 - 383
3	3	ASN	ASN	PHE	PHE	C	C	300 - 381	300 - 381
4	3	ASN	ASN	ASP	ASP	D	D	300 - 383	300 - 383
1	4	LEU	LEU	GLU	GLU	B	B	390 - 469	390 - 469
2	4	LEU	LEU	GLU	GLU	A	A	390 - 469	390 - 469
3	4	LEU	LEU	GLU	GLU	C	C	390 - 469	390 - 469
4	4	LEU	LEU	GLU	GLU	D	D	390 - 469	390 - 469

NCS ensembles :

ID
1
2
3
4

#1: Protein	Probable aspartokinase / Aspartate kinase Mass: 51457.125 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ0571 / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q57991, aspartate kinase
#2: Chemical	ChemComp-THR / THREONINE Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₄H₉NO₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 71 / 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 Å³/Da / Density % sol: 58.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M ammonium iodide, 2.2M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.7→50 Å / Num. obs: 56798 / % possible obs: 69.1 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / B_iso Wilson estimate: 74.1 Å² / R_merge(I) obs: 0.091 / Net I/σ(I): 18.1
Reflection shell	Resolution: 2.7→2.8 Å / Redundancy: 2 % / R_merge(I) obs: 0.236 / Mean I/σ(I) obs: 3.4 / Num. unique all: 1419

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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
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3.004	data extraction
SERGUI		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3C1M

3c1m

Resolution: 2.72→50 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.898 / SU B: 32.816 / SU ML: 0.32 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29	2872	5.1 %	RANDOM
R_work	0.236	-	-	-
obs	0.239	56187	84.37 %	-
all	-	56798	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 63.799 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.51 Å²	0 Å²	0 Å²
2-	-	-2.44 Å²	0 Å²
3-	-	-	-1.07 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.434 Å	-
Luzzati sigma a	-	0.5325 Å

Refinement step

Cycle: LAST / Resolution: 2.72→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13766	0	56	71	13893

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	13965
X-RAY DIFFRACTION	r_angle_refined_deg	1.124	1.988	18829
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.049	5	1810
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.819	25.105	523
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.698	15	2620
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.142	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	2294
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	9992
X-RAY DIFFRACTION	r_nbd_refined	0.206	0.2	6590
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	9806
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.131	0.2	443
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.207	0.2	40
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.063	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	0.323	1.5	9256
X-RAY DIFFRACTION	r_mcangle_it	0.569	2	14574
X-RAY DIFFRACTION	r_scbond_it	0.737	3	5138
X-RAY DIFFRACTION	r_scangle_it	1.272	4.5	4255

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	B	1221	LOOSE POSITIONAL	0.52	5
1	2	A	1221	LOOSE POSITIONAL	0.51	5
1	3	C	1221	LOOSE POSITIONAL	0.49	5
1	4	D	1221	LOOSE POSITIONAL	0.74	5
1	1	B	1221	LOOSE THERMAL	3.26	10
1	2	A	1221	LOOSE THERMAL	1.32	10
1	3	C	1221	LOOSE THERMAL	2.33	10
1	4	D	1221	LOOSE THERMAL	5.21	10
2	1	B	923	LOOSE POSITIONAL	0.49	5
2	2	A	923	LOOSE POSITIONAL	0.43	5
2	3	C	923	LOOSE POSITIONAL	0.49	5
2	4	D	923	LOOSE POSITIONAL	0.63	5
2	1	B	923	LOOSE THERMAL	2.82	10
2	2	A	923	LOOSE THERMAL	2.67	10
2	3	C	923	LOOSE THERMAL	1.82	10
2	4	D	923	LOOSE THERMAL	4.37	10
3	1	B	561	LOOSE POSITIONAL	0.69	5
3	2	A	561	LOOSE POSITIONAL	0.55	5
3	3	C	561	LOOSE POSITIONAL	0.71	5
3	4	D	561	LOOSE POSITIONAL	0.66	5
3	1	B	561	LOOSE THERMAL	3.17	10
3	2	A	561	LOOSE THERMAL	2.99	10
3	3	C	561	LOOSE THERMAL	1.18	10
3	4	D	561	LOOSE THERMAL	5.44	10
4	1	B	591	LOOSE POSITIONAL	0.54	5
4	2	A	591	LOOSE POSITIONAL	0.54	5
4	3	C	591	LOOSE POSITIONAL	0.79	5
4	4	D	591	LOOSE POSITIONAL	0.61	5
4	1	B	591	LOOSE THERMAL	2.81	10
4	2	A	591	LOOSE THERMAL	3.75	10
4	3	C	591	LOOSE THERMAL	1.4	10
4	4	D	591	LOOSE THERMAL	6.94	10

LS refinement shell

Resolution: 2.72→2.788 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.336	56	-
R_work	0.247	894	-
all	-	950	-
obs	-	1419	20.13 %

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	2.2194	0.5501	-0.2365	3.8704	-0.8522	2.5644	0.17	-0.23	0.3756	0.4484	-0.163	-0.0797	-0.4795	0.0055	-0.007	0.1291	-0.2094	0.0704	0.0823	-0.0539	-0.0733	55.2956	47.6801	32.3694
2	2.5792	0.8	1.7841	3.7563	-0.0761	4.2649	0.0533	0.0819	0.297	-0.239	-0.1993	0.2444	-0.1688	-0.072	0.146	0.0749	-0.0462	-0.0136	-0.0406	0.0282	-0.2238	39.2144	21.1548	22.2723
3	3.0957	1.1504	0.095	4.6091	-0.8976	3.4259	-0.3691	0.3174	-0.2297	-0.1436	0.0547	-0.6778	0.5819	0.0437	0.3144	-0.0376	-0.0865	-0.0969	-0.0566	0.0234	-0.1583	28.5421	-0.9825	-24.0392
4	1.6967	0.3176	-0.0181	1.9293	-0.3214	3.5026	-0.1733	-0.1546	0.3796	0.2766	0.0752	-0.1044	0.0072	-0.1979	0.0981	-0.0051	-0.0199	-0.166	-0.0215	-0.0083	-0.1397	25.2059	7.5793	-11.397
5	2.8157	2.0184	1.5506	3.1118	1.1246	3.5939	0.0407	0.4272	0.071	-0.2642	0.1207	-0.1186	0.0181	0.5008	-0.1614	0.154	0.0501	-0.0056	0.0466	0.0753	-0.2097	43.696	11.4498	10.9715
6	5.2446	1.3958	-2.421	3.3687	-1.9846	5.0486	-0.0658	0.4553	-0.1443	-0.5837	0.4004	-0.0875	0.18	-0.3802	-0.3346	0.2733	-0.2664	-0.0376	0.0298	0.0283	0.1247	49.7883	30.6161	-55.147
7	0.6036	-0.1165	-0.1043	3.7493	0.1221	1.0226	-0.0838	-0.1191	0.3069	-0.2998	0.2393	-0.0224	-0.0639	-0.0887	-0.1555	0.1525	-0.2095	-0.0588	0.1138	0.0061	0.2869	52.2645	44.9722	-43.88
8	1.1261	-1.0211	1.8981	1.787	-0.6047	4.6469	0.0501	-0.2778	-0.7711	0.5879	-0.1281	1.3301	0.8778	-0.8623	0.0781	0.2008	-0.2348	0.124	0.2707	0.2667	1.0946	31.7679	57.9778	-27.3863
9	2.7562	0.5276	-1.15	3.7318	-0.4982	6.139	0.3861	0.4852	-0.3988	-0.4941	-0.1039	0.8148	-0.233	-0.6209	-0.2822	0.3467	0.0245	-0.1976	0.1131	0.0722	0.5961	38.1818	69.9354	-43.6903
10	3.8727	-1.2072	0.9579	4.9661	-1.3664	1.3146	-0.0125	-0.3564	0.5397	0.7452	0.0298	-0.193	-0.7393	-0.2491	-0.0174	0.7161	0.25	0.4705	0.1804	0.1458	0.3202	34.1517	84.3612	9.6346
11	0.3421	0.5014	-1.1412	3.0553	-0.3009	4.6168	0.0417	0.1478	-0.1495	0.361	0.238	0.6422	-0.1566	-0.8355	-0.2796	0.2087	0.2563	0.3836	0.3711	0.4246	0.6427	24.761	79.4834	-5.0978
12	2.9058	-1.9893	-1.4396	5.6857	0.6094	4.674	-0.1498	-0.4469	-0.4545	0.1574	0.4348	0.4931	-0.2419	0.1958	-0.285	-0.1244	-0.0238	0.0092	-0.0883	0.22	0.1998	42.6717	74.4073	-26.3938

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	2 - 289	2 - 289
2	X-RAY DIFFRACTION	2	A	A	290 - 469	290 - 469
3	X-RAY DIFFRACTION	3	B	B	2 - 107	2 - 107
4	X-RAY DIFFRACTION	4	B	B	108 - 287	108 - 287
5	X-RAY DIFFRACTION	5	B	B	288 - 469	288 - 469
6	X-RAY DIFFRACTION	6	C	C	2 - 103	2 - 103
7	X-RAY DIFFRACTION	7	C	C	104 - 345	104 - 345
8	X-RAY DIFFRACTION	8	C	C	346 - 393	346 - 393
9	X-RAY DIFFRACTION	9	C	C	394 - 469	394 - 469
10	X-RAY DIFFRACTION	10	D	D	3 - 128	3 - 128
11	X-RAY DIFFRACTION	11	D	D	129 - 279	129 - 279
12	X-RAY DIFFRACTION	12	D	D	280 - 469	280 - 469

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