PDB-6dzs: Mycobacterial homoserine dehydrogenase ThrA in complex with NADP

ID or keywords:

Entry

Database: PDB / ID: 6dzs

Title

Mycobacterial homoserine dehydrogenase ThrA in complex with NADP

Components

Homoserine dehydrogenase

Keywords

OXIDOREDUCTASE / methionine biosynthesis / threonine biosynthesis / Rv1294 / L-homoserine / L-aspartate 4-semialdehyde / NAD / NADP

Function / homology

Function and homology information

homoserine dehydrogenase / homoserine dehydrogenase activity / L-threonine biosynthetic process / methionine biosynthetic process / isoleucine biosynthetic process / NADP binding
Similarity search - Function

Biological species

Mycobacterium hassiacum

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.62 Å

Authors

Chaton, C.T. / Rodriguez, E.S. / Korotkov, K.V.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P20GM103486	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P30GM110787	United States

Citation

Journal: To be Published
Title: Structure of mycobacterial homoserine dehydrogenase ThrA
Authors: Chaton, C.T. / Rodriguez, E.S. / Korotkov, K.V.

History

Deposition	Jul 5, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 18, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2020	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

-
Download

PDBx/mmCIF format	6dzs.cif.gz	898.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6dzs.ent.gz	767.9 KB	Display	PDB format
PDBx/mmJSON format	6dzs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6dzs_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	6dzs_full_validation.pdf.gz	1.6 MB	Display
Data in XML	6dzs_validation.xml.gz	55.7 KB	Display
Data in CIF	6dzs_validation.cif.gz	75.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dz/6dzs ftp://data.pdbj.org/pub/pdb/validation_reports/dz/6dzs	HTTPS FTP

-
Related structure data

Related structure data	3mtjS S: Starting model for refinement
Similar structure data	3mtj-2 4d4k-1 4q7h-1 1k6m-1 3eoy-2 6m77-d 6adm-d 6u6z-2 6adr-d 6adl-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

-
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: Homoserine dehydrogenase

B: Homoserine dehydrogenase

C: Homoserine dehydrogenase

D: Homoserine dehydrogenase

hetero molecules

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

1

A: Homoserine dehydrogenase

B: Homoserine dehydrogenase

hetero molecules

defined by author&software
Evidence: gel filtration, dimers AB and CD
92.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Homoserine dehydrogenase

D: Homoserine dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	93.800, 110.320, 97.530
Angle α, β, γ (deg.)	90.000, 91.830, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Homoserine dehydrogenase / ThrA Mass: 45516.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: UNP residues 3-440 Source: (gene. exp.) Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849) (bacteria) Strain: DSM 44199 / CIP 105218 / JCM 12690 / 3849 / Gene: hom, C731_3131 / Plasmid: pCDF-NT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2(DE3) / References: UniProt: K5BJC9, homoserine dehydrogenase
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.77 Å³/Da / Density % sol: 55.6 % / Description: rectangular prism
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M HEPES, pH 7.0, 1.0 M lithium chloride, 20% PEG6000

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-BM / Wavelength: 1 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2017
Details: Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror

Radiation

Monochromator: double crystal liquid nitrogen-cooled Si(220)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.62→44.583 Å / Num. obs: 59735 / % possible obs: 99.9 % / Redundancy: 5.101 % / B_iso Wilson estimate: 64.96 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.105 / R_rim(I) all: 0.118 / Χ²: 1.049 / Net I/σ(I): 13.55

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.62-2.69	5.119	1.428	1.27	4382	0.489	1.596	100
2.69-2.76	5.123	1.06	1.73	4301	0.602	1.186	99.9
2.76-2.84	5.142	0.856	2.19	4187	0.703	0.959	100
2.84-2.93	5.134	0.693	2.85	4042	0.775	0.777	100
2.93-3.03	5.141	0.51	4.04	3930	0.876	0.574	100
3.03-3.13	5.159	0.393	5.22	3808	0.906	0.441	100
3.13-3.25	5.148	0.295	6.9	3678	0.942	0.332	100
3.25-3.38	5.128	0.226	8.83	3509	0.958	0.255	100
3.38-3.53	5.133	0.166	11.68	3390	0.979	0.187	99.9
3.53-3.71	5.114	0.132	14.32	3246	0.984	0.148	100
3.71-3.91	5.108	0.1	17.64	3104	0.992	0.113	100
3.91-4.14	5.078	0.076	21.97	2903	0.995	0.085	100
4.14-4.43	5.036	0.063	25.28	2765	0.996	0.071	100
4.43-4.78	5.031	0.05	29.54	2540	0.998	0.056	100
4.78-5.24	5.063	0.048	30.52	2375	0.997	0.054	100
5.24-5.86	5.052	0.054	27.81	2132	0.997	0.061	99.9
5.86-6.76	5.045	0.051	29.3	1887	0.997	0.057	100
6.76-8.29	5.013	0.033	37.32	1610	0.998	0.037	99.9
8.29-11.72	4.95	0.024	44.58	1247	0.999	0.028	99.8
11.72-44.583	4.763	0.024	44.76	699	0.999	0.027	98

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	5.49 Å	73.05 Å
Translation	5.49 Å	73.05 Å

-
Processing

Software

Name	Version	Classification
PHENIX	dev_3139	refinement
XSCALE	VERSION Nov 1, 2016 BUILT=20170215	data scaling
PHASER	2.7.17	phasing
PDB_EXTRACT	3.24	data extraction
XDS	VERSION Nov 1, 2016 BUILT=20170215	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3MTJ

3mtj

Resolution: 2.62→44.583 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.14 / Phase error: 28.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2446	3191	5.34 %	random selection
R_work	0.2061	-	-	-
obs	0.2082	59714	99.24 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 183.16 Å² / B_iso mean: 76.7407 Å² / B_iso min: 28.53 Å²

Refinement step

Cycle: final / Resolution: 2.62→44.583 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12415	0	292	48	12755
B_iso mean	-	-	82.89	49.56	-
Num. residues	-	-	-	-	1712

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	f_bond_d	0.003	0.041	12772
X-RAY DIFFRACTION	f_angle_d	0.534	4.414	17426
X-RAY DIFFRACTION	f_chiral_restr	0.045	0.199	2133
X-RAY DIFFRACTION	f_plane_restr	0.004	0.048	2348
X-RAY DIFFRACTION	f_dihedral_angle_d	10.242	179.975	7797

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.62-2.6498	0.3791	192	0.359	3671	3863	99
2.6498-2.6809	0.3472	174	0.3429	3774	3948	99
2.6809-2.7136	0.3122	151	0.3414	3675	3826	100
2.7136-2.748	0.3539	192	0.3362	3707	3899	100
2.748-2.7841	0.3674	177	0.3284	3740	3917	100
2.7841-2.8223	0.3381	190	0.3425	3704	3894	100
2.8223-2.8626	0.3968	205	0.3378	3688	3893	99
2.8626-2.9053	0.3646	197	0.3177	3691	3888	100
2.9053-2.9507	0.3177	217	0.3134	3717	3934	100
2.9507-2.999	0.3448	241	0.2893	3587	3828	100
2.999-3.0507	0.3602	279	0.2858	3693	3972	100
3.0507-3.1062	0.2985	220	0.2721	3653	3873	100
3.1062-3.1659	0.338	237	0.2729	3658	3895	100
3.1659-3.2305	0.3205	187	0.2801	3742	3929	100
3.2305-3.3008	0.3648	195	0.2838	3662	3857	100
3.3008-3.3775	0.2857	225	0.2648	3690	3915	99
3.3775-3.462	0.2354	217	0.2452	3709	3926	100
3.462-3.5555	0.3263	233	0.2418	3638	3871	99
3.5555-3.6601	0.2846	218	0.2249	3673	3891	99
3.6601-3.7782	0.2611	215	0.2225	3672	3887	99
3.7782-3.9131	0.2437	208	0.2002	3692	3900	99
3.9131-4.0697	0.2503	217	0.183	3673	3890	99
4.0697-4.2548	0.1764	232	0.1701	3620	3852	99
4.2548-4.4789	0.1704	254	0.1537	3579	3833	99
4.4789-4.7592	0.1823	212	0.1361	3664	3876	99
4.7592-5.1262	0.168	225	0.145	3671	3896	99
5.1262-5.6412	0.2282	219	0.1615	3586	3805	98
5.6412-6.4554	0.2186	209	0.1787	3678	3887	99
6.4554-8.125	0.1646	168	0.1428	3701	3869	99
8.125-44.5893	0.1506	121	0.1302	3709	3830	98

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	2.0727	-0.4545	0.2524	1.1887	-0.2377	1.1993	0.0259	-0.0747	-0.2166	0.1463	0.0032	-0.1821	0.2003	0.1348	-0.0379	0.4279	0.0095	-0.0146	0.2847	0.0089	0.4059	1.7818	-17.1756	-8.1158
2	0.4273	0.8589	0.1417	1.9978	0.641	0.7391	-0.0052	0.0735	-0.2929	0.1517	0.1111	-0.5243	0.0935	0.5776	-0.129	0.6385	-0.0196	-0.0313	0.7534	-0.0272	0.6081	-4.4251	-5.048	3.3496
3	3.163	-0.4244	-0.0155	3.4993	-0.3372	3.2728	0.009	-0.1132	-0.0494	0.0949	0.1118	0.4075	0.0726	-0.3429	-0.0994	0.4232	0.0505	0.0045	0.5588	0.0129	0.4765	-33.5951	-6.3996	-16.627
4	1.7367	0.4303	0.0026	2.8063	0.5484	2.4305	0.1452	-0.2202	-0.009	0.219	0.0752	-0.6712	-0.1897	0.3542	-0.2151	0.552	-0.0568	-0.1027	0.5198	-0.0811	0.6879	17.8451	13.3634	-3.7873
5	2.4965	-0.1704	0.7407	2.215	-0.6764	2.6656	-0.0883	0.223	0.4747	-0.1264	0.0749	-0.2858	-0.2168	0.0512	0.0151	0.3823	-0.0547	0.0789	0.3907	0.0355	0.5905	11.6455	2.2891	-28.4404
6	1.3352	-0.9295	-0.9696	1.6961	1.3733	1.1922	-0.1573	-0.1684	0.1455	0.322	0.1976	-0.5645	0.1395	0.3813	-0.0427	0.576	-0.0059	-0.0618	0.52	-0.008	0.749	19.2053	-1.0963	-13.1437
7	2.2583	0.1211	0.8154	2.1909	0.6443	2.703	-0.1897	0.4842	0.283	-0.4223	-0.0057	-0.2734	-0.4722	0.7949	0.1886	0.6699	-0.066	0.1756	0.9186	0.1621	0.711	13.8981	1.2791	-53.4631
8	0.9005	-0.7572	-0.0316	1.9839	1.028	1.5207	-0.1219	0.0889	-0.2912	-0.2421	-0.1028	0.5877	0.4531	-0.4627	0.1869	0.8499	-0.3214	-0.0616	0.8859	0.0219	0.8058	-54.8103	-19.1117	24.717
9	3.3538	0.1105	0.681	2.8153	0.5315	1.9226	0.0523	0.4023	-0.2846	-0.749	0.1702	0.0594	0.1784	-0.2278	-0.2156	0.9297	-0.2627	-0.049	0.8136	0.1059	0.5376	-41.6973	-12.8795	16.3005
10	1.5848	-0.2713	0.7257	2.111	-0.2836	1.911	-0.062	-0.0068	-0.2058	-0.3498	0.1491	0.0275	0.4476	-0.1396	-0.0924	0.5981	-0.039	0.0485	0.5001	-0.022	0.3518	-22.8519	-9.6783	31.0328
11	3.3764	1.9611	-0.4333	4.3406	1.0893	1.1205	-0.3542	-0.0613	-0.0149	-0.36	0.2995	0.5582	0.4138	-0.2002	0.0413	0.7205	-0.1276	-0.0718	0.7128	0.1017	0.5768	-41.5265	-4.0865	29.0637
12	1.732	0.2151	1.6505	0.9026	-0.2122	1.6005	0.0628	0.4339	-0.0564	-0.2818	-0.061	-0.2196	0.216	0.2852	0.0411	0.696	0.0866	0.137	0.8471	0.0516	0.5222	-5.7543	-9.2156	29.7604
13	2.5483	-0.7807	-0.0683	3.5382	-0.6581	3.1277	0.0033	0.1826	0.5232	-0.3328	0.1552	0.285	-0.2054	-0.4587	-0.1514	0.5242	-0.0484	-0.0811	0.7446	0.1311	0.6591	-44.2725	21.7873	21.668
14	2.2246	0.2266	1.3108	2.7775	0.2306	4.0593	-0.219	-0.1111	0.1458	-0.0081	0.2712	0.0486	-0.3343	-0.534	-0.0467	0.4506	0.1005	0.0201	0.5655	0.0312	0.409	-39.6485	9.9587	46.8371
15	0.9783	0.2092	-0.5418	0.705	-0.7077	0.8548	-0.2056	0.269	0.0448	-0.4058	0.3255	0.1809	0.3373	-0.7185	-0.1314	0.6839	-0.1078	-0.1182	0.945	0.0783	0.6601	-48.933	8.6039	30.4844
16	2.5893	0.009	0.5432	2.9514	-0.5204	2.8326	-0.1078	0.0793	0.27	0.1956	-0.0122	0.1185	-0.3976	-0.6586	0.1229	0.6127	0.2088	-0.0037	0.7573	0.0246	0.4943	-42.1097	8.9187	71.4447

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 330 )	A	4 - 330
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 331 through 353 )	A	331 - 353
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 354 through 438 )	A	354 - 438
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 6 through 140 )	B	6 - 140
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 141 through 309 )	B	141 - 309
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 310 through 354 )	B	310 - 354
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 355 through 438 )	B	355 - 438
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 6 through 76 )	C	6 - 76
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 77 through 140 )	C	77 - 140
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 141 through 295 )	C	141 - 295
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 296 through 329 )	C	296 - 329
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 330 through 438 )	C	330 - 438
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 6 through 140 )	D	6 - 140
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 141 through 309 )	D	141 - 309
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 310 through 353 )	D	310 - 353
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 354 through 438 )	D	354 - 438

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi