PDB-3mtj: The Crystal Structure of a Homoserine Dehydrogenase from Thiobaci...

ID or keywords:

Entry

Database: PDB / ID: 3mtj

Title

The Crystal Structure of a Homoserine Dehydrogenase from Thiobacillus denitrificans to 2.15A

Components

Homoserine dehydrogenase

Keywords

OXIDOREDUCTASE / Rossmann-fold / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative

Function / homology

Function and homology information

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

Biological species

Thiobacillus denitrificans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.15 Å

Authors

Stein, A.J. / Cui, H. / Chin, S. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The Crystal Structure of a Homoserine Dehydrogenase from Thiobacillus denitrificans to 2.15A
Authors: Stein, A.J. / Cui, H. / Chin, S. / Savchenko, A. / Joachimiak, A.

History

Deposition	Apr 30, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 12, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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	3mtj.cif.gz	182.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3mtj.ent.gz	146.5 KB	Display	PDB format
PDBx/mmJSON format	3mtj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mt/3mtj ftp://data.pdbj.org/pub/pdb/validation_reports/mt/3mtj	HTTPS FTP

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Related structure data

Similar structure data	4p0r-d 5e5w-1 3zep-d 2i52-3 1kti-1 4jun-d 6aqo-d 5mvf-1 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
Other databases	TargetDB: APC40289

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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: Homoserine dehydrogenase

hetero molecules

48.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Homoserine dehydrogenase

hetero molecules

A: Homoserine dehydrogenase

hetero molecules

A: Homoserine dehydrogenase

hetero molecules

A: Homoserine dehydrogenase

hetero molecules

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

2

A: Homoserine dehydrogenase

hetero molecules

A: Homoserine dehydrogenase

hetero molecules

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

3

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	67.613, 67.613, 224.279
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2

#1: Protein	Homoserine dehydrogenase Mass: 48389.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thiobacillus denitrificans (bacteria) / Strain: ATCC 25259 / Gene: Tbd_0843 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3SKI5, homoserine dehydrogenase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.9 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.5M Ammonium sulfate, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2010

Radiation

Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection

Resolution: 2.15→50 Å / Num. obs: 29384 / % possible obs: 99.8 % / Redundancy: 3.9 % / R_merge(I) obs: 0.088 / Χ²: 1.787 / Net I/σ(I): 8.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.15-2.23	4	0.67	2876	0.966	100
2.23-2.32	3.9	0.422	2869	1.166	100
2.32-2.42	3.9	0.351	2882	0.991	100
2.42-2.55	4	0.278	2876	1.024	100
2.55-2.71	3.9	0.2	2919	1.092	100
2.71-2.92	3.9	0.14	2907	1.217	100
2.92-3.21	3.9	0.093	2931	1.456	100
3.21-3.68	3.9	0.065	2941	1.979	99.9
3.68-4.63	3.8	0.059	3003	3.082	99.8
4.63-50	3.6	0.053	3180	5.067	98

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
MLPHARE		phasing
DM		phasing
ARP/wARP		model building
Coot		model building

Refinement

Resolution: 2.15→46.76 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.922 / SU B: 13.271 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.256	1493	5.1 %	RANDOM
R_work	0.217	-	-	-
obs	0.219	29337	99.82 %	-

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: 43.8 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	0 Å²
2-	-	-0.01 Å²	0 Å²
3-	-	-	0.02 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→46.76 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3202	0	15	113	3330

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	3271
X-RAY DIFFRACTION	r_angle_refined_deg	1.252	1.977	4456
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.686	5	432
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.51	23.359	131
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.479	15	523
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.497	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	540
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	2439
X-RAY DIFFRACTION	r_mcbond_it	0.393	1.5	2139
X-RAY DIFFRACTION	r_mcangle_it	0.716	2	3418
X-RAY DIFFRACTION	r_scbond_it	1.583	3	1132
X-RAY DIFFRACTION	r_scangle_it	2.411	4.5	1036

LS refinement shell

Resolution: 2.15→2.206 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.313	113	-
R_work	0.272	2000	-
all	-	2113	-
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	3.9836	15.3881	-13.9866	38.5764	-23.3306	21.445	0.3191	0.2945	0.6953	0.1239	0.9566	2.365	-0.6703	-0.6049	-1.2758	0.2366	-0.005	-0.0721	0.2379	-0.0478	0.4282	18.9433	36.1494	50.1633
2	2.905	0.5191	-1.9324	3.8732	2.0474	2.6467	0.0957	0.0048	0.1546	0.1982	-0.1588	0.2211	0.0539	-0.1652	0.0632	0.0189	-0.0347	0.0121	0.1253	-0.0427	0.1758	15.0694	24.0658	67.926
3	2.8856	2.8173	-0.4035	7.5753	-1.2396	1.9056	0.1448	-0.1995	0.1185	0.5737	-0.1231	0.472	0.01	-0.202	-0.0217	0.0511	-0.0244	0.0423	0.219	-0.0581	0.1939	13.8115	25.4369	65.2219
4	3.5944	1.0817	0.5314	3.9703	1.2483	4.5338	0.1512	0.1152	-0.1926	0.1079	-0.0999	0.2911	-0.0039	-0.1778	-0.0514	0.0149	-0.0284	0.0035	0.0797	-0.0289	0.133	15.7723	15.3413	60.5767
5	2.2969	0.4731	0.583	0.6689	0.4197	3.2807	0.1166	0.0882	-0.2753	0.0227	-0.113	-0.0652	0.1377	-0.0093	-0.0036	0.037	-0.0134	-0.0105	0.1065	-0.0119	0.1945	29.7263	15.4577	66.0551
6	3.0737	0.5961	-0.7143	3.2669	-1.8512	2.7075	0.0487	-0.1762	-0.1013	0.1509	-0.1223	-0.0662	0.1991	0.0781	0.0737	0.1048	-0.0533	-0.0222	0.0894	-0.0249	0.1113	36.5071	24.7309	82.6329
7	5.2438	-2.0332	-2.9265	2.6907	4.2957	10.4409	-0.1867	-0.109	-0.2826	0.3916	-0.2042	0.5632	0.4563	-1.1654	0.3909	0.4625	-0.1946	0.1029	0.4996	0.1332	0.4924	21.4056	13.7061	95.8487
8	3.7185	-0.3292	0.1683	1.5031	0.6104	3.6624	0.0254	-0.0993	-0.1675	0.1791	-0.0528	0.1626	0.5216	-0.0828	0.0273	0.1207	-0.0107	-0.0262	0.0937	0.0203	0.1145	35.6096	15.6625	79.8358
9	3.0121	4.8853	-6.5147	4.0657	-6.991	20.7959	-0.0662	0.2437	-0.0489	-0.1649	0.3855	0.1761	0.2356	0.049	-0.3193	0.3257	0.0319	0.0107	0.2002	-0.039	0.3003	41.6713	10.0691	76.8337
10	3.2027	-0.5819	-2.2343	1.1905	-8.1672	19.0733	-0.3688	-2.1498	-0.666	0.538	0.2921	0.4848	1.0677	0.4172	0.0766	0.731	0.013	0.0521	1.1726	0.3322	0.2038	34.9723	14.615	102.9512
11	5.1415	-0.6738	-2.0281	2.9242	0.0172	4.6805	0.0983	-0.4133	0.0349	0.3305	0.0618	-0.1413	0.2178	0.3149	-0.1601	0.1823	-0.0044	-0.0859	0.1742	0.0507	0.1286	43.055	18.0482	88.2665
12	1.8606	-2.3331	3.4142	18.8089	1.5209	4.2022	-0.28	-0.7004	0.7021	1.3176	0.1338	-0.7271	-0.1906	-0.4626	0.1462	0.2917	-0.11	-0.0208	0.57	-0.1471	0.1804	36.8955	27.4685	96.1153
13	23.5345	20.5366	-8.8022	17.3552	-7.0753	9.6516	0.1396	0.0623	1.0306	0.1568	-0.0385	0.5576	-0.0982	-0.3364	-0.1012	0.1371	-0.001	-0.0789	0.0892	0.0118	0.211	39.8483	29.5977	83.482
14	6.2885	2.9166	6.6212	3.6283	2.7999	6.1337	0.1451	-0.554	-0.1912	0.4031	-0.0742	0.1876	0.099	-0.4113	-0.0709	0.0737	-0.047	0.0314	0.1766	-0.0002	0.1797	25.7757	28.0127	78.0756
15	15.8622	-1.1303	-3.8493	4.1938	1.5063	-0.584	-0.0189	0.752	-0.1495	-0.2306	-0.0664	-0.0393	0.0083	-0.1147	0.0853	0.0652	0.038	-0.0113	0.1625	0.0236	0.1215	31.4721	29.4288	56.3389
16	0.5347	-0.6607	1.241	0.3075	-0.5485	5.1501	-0.0249	-0.073	-0.0354	0.1602	0.0456	-0.0489	0.9	0.2294	-0.0207	0.3117	0.0298	-0.0684	0.3207	0.0587	0.2609	45.9397	15.1678	80.0006
17	5.3299	2.7465	4.7303	7.1411	2.1253	4.2228	0.4448	-1.0116	0.3436	0.3705	-0.5774	0.3454	0.8907	0.0945	0.1326	0.7792	0.4458	-0.1807	0.79	-0.033	0.302	52.0643	9.028	109.4605
18	3.0164	0.6922	-1.6571	5.6356	-1.8612	16.3232	0.1773	-0.2711	0.1152	0.3494	0.0855	0.1826	0.4872	0.1116	-0.2628	0.3484	0.0594	-0.1811	0.2607	0.0472	0.2191	48.6352	11.2027	103.494
19	10.0552	-4.1996	0.4591	0.4861	-2.1217	16.6664	-0.1353	-0.815	-0.9039	-0.012	0.1458	0.4628	2.1195	0.5168	-0.0105	1.2779	0.2185	-0.084	0.3018	0.1174	0.3108	48.9686	1.3135	104.4708
20	7.279	-9.5003	1.7343	30.2764	-5.0711	17.1945	0.5053	-0.6874	-0.1346	0.557	-0.3597	0.2458	0.6904	0.7055	-0.1456	0.2776	0.0382	-0.1068	0.4172	0.0065	0.0804	43.7562	16.9427	96.0087

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-2 - 3
2	X-RAY DIFFRACTION	2	A	4 - 24
3	X-RAY DIFFRACTION	3	A	25 - 54
4	X-RAY DIFFRACTION	4	A	55 - 80
5	X-RAY DIFFRACTION	5	A	81 - 138
6	X-RAY DIFFRACTION	6	A	139 - 167
7	X-RAY DIFFRACTION	7	A	168 - 194
8	X-RAY DIFFRACTION	8	A	195 - 214
9	X-RAY DIFFRACTION	9	A	215 - 223
10	X-RAY DIFFRACTION	10	A	224 - 242
11	X-RAY DIFFRACTION	11	A	243 - 265
12	X-RAY DIFFRACTION	12	A	266 - 278
13	X-RAY DIFFRACTION	13	A	279 - 292
14	X-RAY DIFFRACTION	14	A	293 - 312
15	X-RAY DIFFRACTION	15	A	313 - 329
16	X-RAY DIFFRACTION	16	A	330 - 356
17	X-RAY DIFFRACTION	17	A	357 - 386
18	X-RAY DIFFRACTION	18	A	393 - 408
19	X-RAY DIFFRACTION	19	A	409 - 426
20	X-RAY DIFFRACTION	20	A	427 - 435

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