PDB-4kdf: Crystal Structure of Thermus thermophilus Malate Dehydrogenase in...

ID or keywords:

Entry

Database: PDB / ID: 4kdf

Title

Crystal Structure of Thermus thermophilus Malate Dehydrogenase in Complex with NAD

Components

Malate dehydrogenase

Keywords

OXIDOREDUCTASE / Dehydrogenase

Function / homology

Function and homology information

malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.356 Å

Authors

Hsu, C.-H. / Hong, C.-H. / Chang, Y.-Y.

Citation

Journal: Plos One / Year: 2013
Title: Crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding.
Authors: Hung, C.H. / Hwang, T.S. / Chang, Y.Y. / Luo, H.R. / Wu, S.P. / Hsu, C.H.

History

Deposition	Apr 25, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	4kdf.cif.gz	492 KB	Display	PDBx/mmCIF format
PDB format	pdb4kdf.ent.gz	415.5 KB	Display	PDB format
PDBx/mmJSON format	4kdf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4kdf_validation.pdf.gz	472.5 KB	Display	wwPDB validaton report
Full document	4kdf_full_validation.pdf.gz	482.8 KB	Display
Data in XML	4kdf_validation.xml.gz	46.7 KB	Display
Data in CIF	4kdf_validation.cif.gz	65.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kd/4kdf ftp://data.pdbj.org/pub/pdb/validation_reports/kd/4kdf	HTTPS FTP

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Related structure data

Related structure data	4kdeSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1gv0-d 4tvo-d 1wze-d 6b3y-d 1bdm-d 6itk-d 1y7t-d 1wzi-d 2hjr-12 6um4-5 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	#154 - Oct 2012 Citric Acid Cycle similarity (10) #102 - Jun 2008 Lactate Dehydrogenase similarity (6) #142 - Oct 2011 PDB Pioneers similarity (6)

Deposited unit

A: Malate dehydrogenase

B: Malate dehydrogenase

C: Malate dehydrogenase

D: Malate dehydrogenase

hetero molecules

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

1

A: Malate dehydrogenase

D: Malate dehydrogenase

hetero molecules

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

2

B: Malate dehydrogenase

C: Malate dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	96.601, 114.617, 144.077
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Malate dehydrogenase Mass: 37150.695 Da / Num. of mol.: 4 / Fragment: Malate Dehydrogenase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: mdh / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10584, malate dehydrogenase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.68 Å³/Da / Density % sol: 54.17 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 22.5% PEG 4000, 0.1M Tris-HCl, 0.2M MgCl2, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.356→24.27 Å / Num. all: 66788 / Num. obs: 66054 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.8 %
Reflection shell	Resolution: 2.356→2.44 Å / % possible all: 92.1

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4KDE

4kde

Resolution: 2.356→24.27 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 33.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2316	1994	3.03 %
R_work	0.1833	-	-
obs	0.1847	65760	98.61 %
all	-	66054	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.356→24.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9638	0	50	325	10013

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9850
X-RAY DIFFRACTION	f_angle_d	1.035	13356
X-RAY DIFFRACTION	f_dihedral_angle_d	14.113	3624
X-RAY DIFFRACTION	f_chiral_restr	0.039	1514
X-RAY DIFFRACTION	f_plane_restr	0.005	1740

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 (%)
2.356-2.4149	0.3172	129	0.239	4148	X-RAY DIFFRACTION	91
2.4149-2.4801	0.2659	138	0.223	4393	X-RAY DIFFRACTION	97
2.4801-2.553	0.2788	142	0.2248	4523	X-RAY DIFFRACTION	99
2.553-2.6353	0.2886	141	0.213	4556	X-RAY DIFFRACTION	100
2.6353-2.7294	0.2674	142	0.2113	4558	X-RAY DIFFRACTION	100
2.7294-2.8385	0.2815	145	0.2011	4601	X-RAY DIFFRACTION	100
2.8385-2.9675	0.267	142	0.1973	4549	X-RAY DIFFRACTION	100
2.9675-3.1236	0.2356	144	0.1935	4595	X-RAY DIFFRACTION	100
3.1236-3.3189	0.2664	143	0.1927	4563	X-RAY DIFFRACTION	100
3.3189-3.5744	0.2326	144	0.1862	4624	X-RAY DIFFRACTION	100
3.5744-3.9327	0.2234	144	0.17	4624	X-RAY DIFFRACTION	100
3.9327-4.4987	0.214	146	0.1505	4635	X-RAY DIFFRACTION	100
4.4987-5.656	0.1587	146	0.1597	4685	X-RAY DIFFRACTION	100
5.656-24.2712	0.2127	148	0.1756	4712	X-RAY DIFFRACTION	97

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	3.758	0.569	-1.3218	3.4201	-0.5436	1.804	-0.2804	-0.6259	0.2379	0.0091	0.0345	0.0908	-0.4612	0.0206	0.0974	0.6561	0.164	0.0016	0.2463	-0.0266	0.2701	67.7444	59.9511	108.8216
2	1.4819	-0.297	0.3774	1.8934	0.2819	2.2452	0.0615	0.1123	0.1698	-0.3418	-0.0587	0.1018	-0.496	-0.1761	-0.047	0.7347	0.179	-0.0096	0.3044	0.0029	0.2971	64.5727	64.6788	103.6089
3	1.7693	-0.4172	1.2647	3.5775	0.9114	4.8411	0.0804	0.1364	0.1387	-0.6038	-0.0887	-0.2449	-0.3707	0.0103	-0.0197	0.8096	0.156	0.0086	0.2868	-0.0091	0.2875	69.1823	57.8841	90.8781
4	1.6083	0.1772	-1.0023	5.2758	0.348	2.1588	0.0133	0.0001	-0.0769	-0.2217	-0.0929	0.0615	0.2048	0.0171	0.1331	0.7139	0.1386	-0.023	0.2873	-0.0215	0.2691	68.6035	32.1409	98.971
5	0.5464	0.2649	-0.4675	2.5826	0.0336	2.3773	0.0451	0.076	0.0384	-0.4729	-0.077	0.0034	-0.0194	0.1757	0.0679	0.5767	0.1382	0.0084	0.2991	-0.0169	0.2308	70.0861	45.8363	97.2397
6	0.3534	0.5592	-0.0073	3.5358	1.2552	1.9037	0.0831	0.0815	-0.0762	-0.7918	-0.0436	0.2356	-0.0275	0.0884	-0.033	0.8836	0.1065	-0.0177	0.3813	0.0038	0.309	68.0554	43.5739	83.8206
7	5.9223	0.4697	-2.8655	3.0196	-1.5088	2.7601	-0.5865	0.112	0.0876	-0.0342	0.3395	0.0501	-0.0265	0.0011	0.2806	0.662	-0.0913	0.0181	0.2354	-0.0358	0.2364	19.5861	59.8853	109.4276
8	2.0321	0.0217	-0.0974	2.1553	-0.0152	2.2801	0.1387	0.1133	0.1107	-0.2265	-0.0688	0.0124	-0.4275	-0.1742	-0.0401	0.779	-0.081	0.0129	0.303	0.0074	0.2999	17.2691	64.6295	108.0168
9	5.8702	5.8122	2.0697	6.2306	2.546	3.1688	-0.1425	1.5484	0.7244	-0.6202	0.2579	0.9366	-0.2938	-0.2429	-0.0723	0.9432	0.0797	-0.079	0.4746	0.0551	0.4665	12.5751	64.6967	90.5234
10	3.3534	0.2945	1.7432	7.0315	-0.7509	6.2219	0.1751	0.0757	0.0712	-0.6409	-0.0702	-0.2345	-0.3491	-0.0832	-0.1156	0.803	-0.0955	0.0437	0.377	0.0199	0.2931	20.8687	57.864	91.5179
11	1.8521	0.5213	-2.4674	2.4158	-0.4711	3.2027	0.0625	-0.1826	-0.0498	0.0439	-0.1616	-0.0246	0.3758	0.2018	0.0705	0.7486	-0.0922	-0.0425	0.3094	-0.0398	0.2553	22.2949	35.0876	103.4184
12	4.9943	-1.9526	0.0166	4.6595	1.143	3.0977	-0.1454	-0.1475	0.063	-0.3123	-0.0329	0.1144	0.3142	-0.1111	0.1794	0.7349	-0.1253	-0.0121	0.3852	-0.0137	0.278	18.8965	30.0204	96.9584
13	3.6239	0.9485	-0.6685	2.1318	0.0744	1.68	-0.0469	-0.2251	-0.0139	-0.0968	-0.0246	0.2453	-0.0247	-0.1599	0.056	0.6336	-0.0905	0.0113	0.3155	-0.0358	0.3149	15.5201	46.8185	105.7729
14	1.5529	0.5263	0.7644	2.1444	0.2552	2.2112	0.0724	0.1609	0.127	-0.459	0.0309	-0.1451	0.0507	0.1321	-0.0591	0.7445	-0.0879	0.0663	0.2664	-0.0094	0.2615	27.2363	44.9559	90.9948
15	0.7839	0.2709	0.0646	6.1113	0.8935	1.7122	0.3414	0.1944	0.0028	-0.9889	-0.2364	0.4654	0.1411	-0.1373	-0.0697	0.8901	-0.1132	0.0088	0.4137	0.0185	0.2985	19.7137	43.5959	84.4391
16	7.2821	-2.2562	-0.0834	2.8308	1.1186	4.0686	-1.0878	0.2008	0.4974	0.2283	0.3606	-0.1079	-0.2878	-0.1938	0.5739	0.8087	-0.0972	-0.1031	0.243	0.0214	0.3324	18.848	40.063	125.526
17	1.3342	0.1231	0.4509	0.9234	-0.5211	1.3071	0.1642	0.2886	0.082	-0.7609	-0.2365	-0.3754	-0.0953	0.1446	0.132	0.6329	-0.1736	-0.0501	0.3156	0.0763	0.3509	13.66	48.55	118.758
18	6.2787	-2.7146	0.0788	2.8903	-1.207	0.8172	0.1334	-0.6148	-1.0561	0.0285	0.0836	0.227	0.2506	0.4441	-0.103	0.6836	-0.134	0.0179	0.3385	-0.0398	0.2707	26.427	45.275	122.19
19	2.3307	-0.3221	-0.5981	2.0744	-0.3103	1.3725	-0.1147	-0.0077	0.3191	-0.056	0.1056	-0.3777	-0.3645	0.394	-0.0653	0.7171	-0.1683	-0.0642	0.3345	-0.0141	0.4032	11.368	38.456	118.07
20	4.1381	1.0635	-0.3492	2.4345	0.019	1.4055	0.1082	0.2341	0.6461	0.7746	0.1499	-0.1321	-1.0385	0.4018	-0.0488	0.9335	-0.2323	-0.1338	0.4881	-0.0422	0.4173	12.674	36.33	131.089
21	1.9972	-5.0185	2.086	3.8055	-2.2483	1.3905	-0.5041	0.4861	-0.1051	-0.0691	0.3187	-0.5311	0.7597	1.203	0.216	0.7145	-0.1027	-0.1257	0.8018	0.0014	0.429	2.181	49.596	129.645
22	8.7608	-6.6118	-1.1281	6.3231	0.3156	2.066	-0.9126	-0.2492	0.7008	0.9494	0.4567	-0.7828	-0.3404	0.471	0.2929	0.7435	-0.2381	-0.2217	0.539	-0.0171	0.4572	3.089	41.842	138.097
23	4.4653	0.1938	2.4	5.6332	1.0925	3.5126	-0.092	-0.2634	0.3111	1.0799	-0.0942	-0.2397	-0.3752	0.0965	0.0395	0.6388	-0.1573	-0.0732	0.3421	-0.004	0.2965	12.769	46.655	139.598
24	0.8973	0.174	-0.1049	3.4952	1.4697	3.0018	0.0169	0.0995	0.0327	0.1179	0.0529	0.1257	0.4076	-0.0817	-0.0396	0.797	-0.0935	-0.0641	0.3228	0.0132	0.288	21.279	68.274	129.166
25	4.0204	2.1129	-2.2002	2.9899	0.6088	3.2127	0.1261	-0.0687	-0.1307	0.5653	-0.1592	-0.1783	0.5156	0.3448	0.0589	0.8576	-0.0215	-0.102	0.3665	0.0653	0.3138	16.963	73.98	134.464
26	2.8589	-2.9232	-1.1595	3.6876	1.1224	1.8212	-0.2097	-0.1805	-0.1387	0.1636	0.1442	-0.1342	0.0382	0.1664	0.0249	0.6708	-0.147	-0.0381	0.2943	0.0187	0.3192	13.662	57.733	124.693
27	2.8214	0.8634	1.5072	1.5253	-0.241	4.0627	-0.2795	-0.064	0.2871	0.7083	0.058	0.0866	-0.2467	-0.1837	0.1925	0.7684	-0.045	-0.0655	0.2955	-0.0529	0.296	22.168	58.796	142.874
28	7.1637	5.7112	2.1395	4.7695	1.7596	2.6512	0.0128	-0.0493	-0.184	0.7263	0.0111	-0.7317	-0.1048	0.0641	-0.0622	0.8535	0.036	-0.1974	0.4092	-0.0249	0.4037	5.826	61.793	146.912
29	4.5144	-0.9116	-1.3195	4.6363	1.0754	4.189	0.0055	0.0068	0.2904	-0.3726	-0.0669	-0.1665	0.3237	0.3193	0.1734	0.4136	0.0571	-0.0488	0.286	0.0563	0.2142	64.684	44.197	121.479
30	2.2497	-0.7464	0.1312	1.815	-0.6798	2.2554	-0.0843	0.0762	0.1516	0.1818	-0.0325	-0.1859	-0.4929	0.1927	0.0769	0.6391	0.0482	-0.0612	0.2638	0.0089	0.2964	60.872	40.169	122.212
31	7.0784	-2.0115	-2.2443	6.167	0.7253	2.8908	-0.1487	-0.7962	0.3922	0.3455	0.0731	-0.6566	-0.8957	0.5058	0.1173	0.911	0.0269	-0.1621	0.4381	0.0202	0.299	56.262	42.662	136.445
32	1.9176	1.3394	0.674	6.956	1.4656	3.3512	0.2845	-0.4057	0.0102	1.0702	-0.4054	-0.1544	-0.2852	-0.279	0.1917	0.831	0.0192	-0.0838	0.3947	0.0136	0.3242	60.074	47.551	141.019
33	0.8476	0.78	0.6586	5.0416	-0.2583	1.9917	0.0091	-0.0915	-0.0353	0.1932	0.0082	0.089	0.2208	-0.2164	0.0036	0.7071	0.1288	0.026	0.299	0.0097	0.249	69.577	68.292	128.544
34	2.7122	1.1925	0.0393	4.0213	0.1713	2.2338	0.2521	0.014	-0.1236	0.4761	-0.2628	-0.1614	0.6294	0.2459	0.0937	0.8458	0.1741	0.0073	0.3517	0.0245	0.2761	65.248	73.995	133.827
35	0.0579	0.2872	-0.2315	3.0692	0.0363	2.5228	-0.1767	-0.1145	-0.0736	-0.0007	-0.022	-0.3192	0.0073	0.3651	0.174	0.5064	0.112	-0.0254	0.3454	0.0337	0.288	61.924	57.72	124.078
36	2.0214	1.187	0.6971	2.6197	-0.5671	3.6512	-0.0611	-0.2972	0.3375	0.783	-0.1895	0.2566	-0.1696	-0.2236	0.2158	0.6751	0.1644	-0.0178	0.3106	-0.0644	0.3099	70.362	58.825	142.293
37	4.1877	3.3767	-0.1731	3.086	-1.0556	2.7249	0.4626	0.0137	-0.1346	1.5563	-0.3903	-0.8831	0.1669	0.6737	-0.0889	0.6651	0.165	-0.1487	0.4796	0.0431	0.5366	54.005	61.699	146.266

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 119 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 120 through 156 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 157 through 224 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 225 through 287 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 288 through 326 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 25 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 26 through 101 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 102 through 119 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 120 through 156 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 157 through 184 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 185 through 224 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 225 through 254 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 255 through 287 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 288 through 326 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1 through 14 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 15 through 25 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 26 through 35 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 36 through 71 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 72 through 85 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 86 through 92 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 101 through 119 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 120 through 156 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 157 through 184 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 185 through 224 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 225 through 254 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 255 through 300 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 301 through 326 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 1 through 25 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 26 through 101 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 102 through 132 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 133 through 156 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 157 through 184 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 185 through 224 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 225 through 254 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 255 through 300 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 301 through 326 )

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