PDB-7q3x: Crystal structure of Malate dehydrogenase from Haloarcula marismo...

ID or keywords:

Entry

Database: PDB / ID: 7q3x

Title

Crystal structure of Malate dehydrogenase from Haloarcula marismortui with Potassium and Chloride ions

Components

Malate dehydrogenase

Keywords

OXIDOREDUCTASE / Malate dehydrogenase / allostery regulation / extremophiles / Haloarcula marismortui

Function / homology

Function and homology information

malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / tricarboxylic acid cycle / cytoplasm
Similarity search - Function

Biological species

Haloarcula marismortui (Halophile)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Bertrand, Q. / Roche, J. / Girard, E. / Madern, D.

Funding support

France, 1items

Citation

Journal: To Be Published
Title: Resurrection of Ancestral Malate Dehydrogenases Reveals the Evolutionary History of Haloarchaeal Proteins.
Authors: Girard, E. / Talon, R. / Bertrand, Q. / Roche, J. / Engilberge, S. / Sacquin-Mora, S. / Blanquart, S. / Zaccai, G. / Gouy, M. / Franzetti, B. / Madern, D.

History

Deposition	Oct 29, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7q3x.cif.gz	494.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7q3x_validation.pdf.gz	8.5 MB	Display	wwPDB validaton report
Full document	7q3x_full_validation.pdf.gz	8.5 MB	Display
Data in XML	7q3x_validation.xml.gz	47.3 KB	Display
Data in CIF	7q3x_validation.cif.gz	69.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q3/7q3x ftp://data.pdbj.org/pub/pdb/validation_reports/q3/7q3x	HTTPS FTP

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Related structure data

Related structure data	2j5kS S: Starting model for refinement
Similar structure data	2j5q-d 2j5r-d 4jco-d 1d3a-1 2j5k-d 4plw-d 4bgu-d 2hlp-1 1o6z-d 6k12-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (7) #154 - Oct 2012 Citric Acid Cycle similarity (7) #142 - Oct 2011 PDB Pioneers similarity (6)

Deposited unit

A: Malate dehydrogenase

B: Malate dehydrogenase

C: Malate dehydrogenase

D: Malate dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: equilibrium centrifugation

Unit cell

Length a, b, c (Å)	128.274, 115.385, 124.828
Angle α, β, γ (deg.)	90.000, 93.020, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-759- HOH

#1: Protein	Malate dehydrogenase Mass: 32706.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haloarcula marismortui (Halophile) / Gene: mdh, rrnAC2706 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07841, malate dehydrogenase
#2: Chemical	... ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 601 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 3.53 Å³/Da / Density % sol: 65.11 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: Protein: 10mg/ml, 50mM Tris pH 7, 2M KCl Cristal Growth: 100mM Tris pH 7.5-7.6 + 60-66% MPD

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979688 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979688 Å / Relative weight: 1
Reflection	Resolution: 1.87→124.65 Å / Num. obs: 145917 / % possible obs: 97.6 % / Redundancy: 3.7 % / CC_1/2: 0.99 / Net I/σ(I): 7.9
Reflection shell	Resolution: 1.87→1.97 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 21941 / CC_1/2: 0.7 / % possible all: 91

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4080	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2J5K

2j5k

Resolution: 1.95→27.42 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.72 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2461	6572	5.03 %
R_work	0.2168	124026	-
obs	0.2183	130598	99.02 %

Solvent computation

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

Displacement parameters

B_iso max: 109.98 Å² / B_iso mean: 39.6493 Å² / B_iso min: 20.37 Å²

Refinement step

Cycle: final / Resolution: 1.95→27.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9194	0	53	601	9848
B_iso mean	-	-	38.91	37.82	-
Num. residues	-	-	-	-	1212

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 (%)
1.95-1.97	0.3649	236	0.3115	4138	4374	100
1.97-2	0.3355	204	0.3171	4142	4346	100
2-2.02	0.3697	217	0.3232	4157	4374	100
2.02-2.05	0.3482	215	0.3325	4148	4363	100
2.05-2.07	0.3369	210	0.3237	4137	4347	99
2.07-2.1	0.3196	205	0.3217	4190	4395	100
2.1-2.13	0.3722	221	0.2998	4082	4303	99
2.13-2.16	0.3076	232	0.2819	4157	4389	100
2.16-2.2	0.2914	224	0.2794	4093	4317	99
2.2-2.23	0.2928	225	0.2715	4162	4387	100
2.23-2.27	0.3087	201	0.2649	4164	4365	99
2.27-2.31	0.3488	235	0.2745	4057	4292	98
2.31-2.36	0.2704	210	0.2626	4146	4356	100
2.36-2.4	0.3086	239	0.2724	4091	4330	98
2.4-2.46	0.3104	249	0.2563	4065	4314	98
2.46-2.51	0.328	202	0.2547	4115	4317	99
2.51-2.58	0.264	197	0.2431	4100	4297	98
2.58-2.65	0.3207	239	0.2458	4098	4337	98
2.65-2.72	0.2719	213	0.2469	4096	4309	98
2.72-2.81	0.255	190	0.2346	4169	4359	99
2.81-2.91	0.2689	204	0.2337	4132	4336	99
2.91-3.03	0.281	216	0.227	4127	4343	99
3.03-3.17	0.2547	231	0.2223	4100	4331	98
3.17-3.33	0.2435	242	0.2143	4092	4334	99
3.33-3.54	0.2165	235	0.1936	4144	4379	99
3.54-3.81	0.1814	185	0.1794	4169	4354	99
3.81-4.2	0.1743	208	0.1634	4163	4371	99
4.2-4.8	0.1708	228	0.1531	4221	4449	99
4.8-6.04	0.2069	237	0.1711	4156	4393	100
6.04-27.42	0.204	222	0.1833	4215	4437	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	3.4544	-0.2146	1.157	3.6688	0.2137	3.6264	0.0097	-0.0193	-0.2052	-0.2656	-0.1026	-0.1999	0.5652	0.1941	0.0916	0.4191	0.0533	0.0461	0.2509	0.0266	0.2196	43.0565	-16.7098	32.7965
2	7.1802	-3.6272	4.6836	3.4796	-1.6954	3.9564	-0.1425	0.629	-0.1979	-0.1862	-0.0895	-0.1678	0.0609	0.4758	0.2409	0.4116	0.0277	0.0916	0.3415	0.0442	0.2496	47.8755	-14.9107	28.1134
3	1.6849	0.4577	-0.3771	4.0612	-2.9046	6.9899	0.0043	-0.1767	-0.2801	0.3161	-0.3	-0.3695	0.7268	0.2004	0.3639	0.4753	0.0113	0.005	0.2638	0.0593	0.2706	45.8689	-21.3359	47.3511
4	4.1579	-0.821	-0.2204	3.9282	-1.3094	7.7687	-0.0024	0.0959	-0.2528	0.1933	-0.1106	-0.4519	0.6403	0.4855	0.1609	0.3637	0.059	-0.0765	0.3164	0.0691	0.3732	53.1015	-18.8975	47.7343
5	1.9275	-0.4667	-0.2789	1.7554	0.0585	1.712	0.0232	-0.1904	-0.0224	0.3501	-0.0823	-0.0453	-0.0331	0.0012	0.064	0.426	-0.0066	-0.009	0.2515	0.0356	0.1948	37.436	-5.1779	54.8829
6	1.6953	-0.729	-1.8161	3.8043	4.7978	9.0142	-0.251	-0.4708	-0.2354	1.5258	-0.0054	0.7126	0.9992	-0.2747	0.1915	0.6726	-0.0322	0.1034	0.4731	0.1091	0.3276	25.4059	-11.6942	59.8501
7	5.3717	3.1003	-0.0644	4.9647	0.1035	0.0798	0.2665	-0.2956	-0.2429	0.4936	-0.3579	-0.0773	0.1767	0.1683	0.0868	0.402	0.0196	0.0027	0.2401	0.0218	0.1971	36.3388	-11.6381	43.3931
8	2.5982	-0.5395	-0.2447	3.8058	-0.6385	3.5461	-0.0013	-0.1429	0.1525	0.4801	-0.1451	-0.2712	-0.3824	0.2417	0.1545	0.435	-0.0594	-0.0897	0.3069	0.0421	0.2724	47.8587	-0.785	55.172
9	1.8849	-0.306	-1.5408	1.8002	2.2961	3.6713	-0.1819	-0.3444	-0.2672	1.0211	-0.0372	-0.112	0.0492	0.2599	0.1357	0.7564	-0.0394	-0.0791	0.4717	0.1158	0.2703	45.3225	-10.7592	67.4758
10	4.3236	0.9925	1.6471	4.4639	0.7372	3.6213	-0.0409	-0.0959	-0.2478	0.3457	-0.0751	0.3193	0.2166	-0.5105	0.1147	0.2957	-0.0374	0.0583	0.2808	-0.0456	0.234	21.5473	-14.3388	39.1418
11	5.38	5.0006	3.4536	6.6101	2.9619	4.39	0.0332	-0.0473	0.1116	0.4871	-0.1926	0.5348	0.123	-0.6282	0.1547	0.3709	0.0511	0.0773	0.3526	-0.0624	0.2851	18.7798	-8.6858	42.3953
12	4.4621	-0.263	0.7298	3.4846	2.0259	6.0387	-0.1489	-0.0425	-0.5134	-0.001	0.3834	0.3507	1.2271	0.3048	-0.2103	0.5098	0.0196	0.0452	0.3966	-0.0627	0.381	17.9731	-24.7865	28.2882
13	3.3916	0.8975	0.3954	4.726	-1.5379	4.7365	0.1305	-0.2815	-0.2478	-0.3404	-0.1248	0.8109	0.6839	-0.8645	0.0053	0.3422	-0.1446	-0.0265	0.5425	-0.1116	0.4717	11.228	-22.4926	26.6297
14	2.4376	0.9297	-0.056	1.4287	0.1515	1.2707	-0.0243	0.1284	-0.2114	-0.1635	-0.1298	0.0822	0.099	-0.1349	0.1668	0.5057	0.0255	-0.0094	0.2845	-0.0607	0.2662	27.71	-14.653	14.2806
15	2.6711	0.5296	-1.3469	0.1505	0.3006	8.38	-0.0125	0.1909	-0.5605	-0.7685	-0.2378	-0.4964	0.6794	0.2639	0.1914	0.8541	0.0767	0.0512	0.2886	-0.0555	0.3898	39.1133	-23.855	13.1782
16	6.0158	-3.838	1.8405	4.7873	-2.6055	1.4729	0.1127	0.0977	-0.2758	-0.266	-0.1585	0.2756	0.3065	-0.0484	0.0776	0.462	-0.0442	0.0169	0.2688	-0.0445	0.222	28.5203	-15.1559	27.4612
17	0.9869	0.6329	0.1106	3.9566	1.1541	4.0619	-0.0433	0.1269	-0.0158	-0.5755	-0.2215	0.3667	-0.0231	-0.3269	0.2547	0.4089	0.0305	-0.0728	0.4012	-0.1041	0.3295	18.0152	-15.1761	9.8811
18	3.3446	0.8466	-0.9593	2.3639	-0.8561	3.4626	-0.0703	0.0439	0.2384	0.3058	-0.0872	-0.2092	-0.5916	0.2782	0.1525	0.5313	-0.0241	-0.0922	0.3022	0.0616	0.2747	44.6316	22.2351	30.7584
19	4.9837	1.6149	-2.5576	2.0591	-0.6963	2.6419	-0.0515	-0.4018	0.2836	0.2818	-0.1389	-0.3068	-0.4485	0.5466	0.1926	0.4967	-0.0534	-0.1295	0.3669	0.0715	0.3085	48.515	19.4441	36.1522
20	1.176	-0.936	-0.0857	5.1949	-4.2482	5.4199	-0.1832	0.008	0.1523	0.3424	0.0323	-0.2231	-0.866	0.042	0.1643	0.6449	-0.0351	-0.0852	0.3358	0.0768	0.3062	49.0448	26.4602	16.2748
21	4.2662	1.1871	-0.1561	3.8135	0.1279	6.3745	0.0195	-0.0891	0.0626	0.0047	-0.2096	-0.6719	-0.5703	0.7014	0.2201	0.4348	-0.0788	-0.073	0.3779	0.1201	0.4119	55.8927	23.1593	16.6284
22	1.5774	0.8132	-0.2523	1.9279	-0.1433	1.481	-0.0494	0.1158	0.0379	-0.3022	-0.1259	-0.0944	-0.0893	0.0047	0.1699	0.5361	0.0559	-0.0322	0.3282	0.0719	0.2154	39.4844	10.7461	8.238
23	1.1222	0.0843	0.3057	0.2268	1.2078	6.4791	0.0023	0.416	0.2875	-1.2395	-0.1571	0.3048	-0.9118	-0.7475	0.1268	0.7921	0.1	-0.1217	0.5118	0.1132	0.3418	28.5512	18.1968	2.4625
24	2.2942	0.6591	-0.832	0.3942	0.1193	0.9138	0.143	0.315	0.2654	-0.3225	-0.2283	-0.0386	-0.3904	0.0381	0.1052	0.6119	0.0415	-0.0776	0.295	0.0475	0.2335	38.2318	17.3088	19.7002
25	2.9946	0.2519	-0.4865	3.6274	0.322	2.7277	-0.0463	0.2745	-0.0492	-0.534	-0.0804	-0.4491	0.4245	0.3471	0.1084	0.4381	0.0747	0.036	0.3514	0.0739	0.2546	49.5603	5.4494	8.5003
26	3.9317	1.1334	0.373	3.9534	0.3839	2.0056	-0.2979	0.7535	0.278	-1.1866	0.068	-0.3073	0.0355	0.3072	0.2257	0.6985	0.0747	0.0355	0.4978	0.1654	0.3092	49.3556	16.2541	-3.0623
27	4.0712	-0.4706	-0.7492	2.2475	0.6906	1.0214	-0.0451	0.2471	0.2861	-0.1795	-0.0715	0.2232	-0.3729	-0.416	0.1241	0.5306	0.14	-0.0797	0.3331	0.0024	0.2725	23.3654	20.7818	22.9003
28	8.564	-4.8649	-2.9225	5.7137	0.8927	4.111	0.192	1.0854	0.0766	-0.2012	-0.5774	0.5053	-0.4826	-0.8479	0.3982	0.4809	0.1148	-0.115	0.4521	-0.0474	0.3275	19.0702	16.7128	19.311
29	3.1062	-0.6515	-0.7652	6.619	2.8836	6.1682	0.0287	-0.1874	0.5043	-0.2141	0.1954	-0.2244	-1.374	0.4224	-0.1754	0.7803	0.0483	-0.02	0.391	-0.029	0.3877	20.1238	31.8869	33.7176
30	2.3285	-1.8514	-0.7702	5.0309	-0.0317	2.748	0.0008	0.1614	0.3801	0.1222	-0.1865	0.4508	-1.0333	-0.8031	0.2252	0.7104	0.3205	0.0054	0.5735	-0.008	0.5174	12.6229	29.9908	34.7783
31	1.7383	-1.0341	0.1048	1.6004	-0.0725	1.5387	-0.0539	-0.0714	0.178	0.3508	-0.0204	0.1028	-0.4571	-0.1311	0.0779	0.6524	0.0651	-0.0027	0.2658	-0.0347	0.3089	28.1126	21.0597	48.2315
32	1.0423	-0.2877	-0.7263	0.3414	-0.5493	2.6443	-0.1335	-0.3355	0.5512	0.6912	-0.1542	-0.0662	-1.2726	0.1196	0.1204	1.0475	-0.0299	-0.09	0.3083	-0.0913	0.4876	39.8109	29.3333	50.1091
33	3.9626	4.8437	-1.3141	5.9666	-1.7711	1.9972	0.1043	-0.1507	0.4767	0.282	-0.1326	0.1865	-0.4325	-0.0122	0.0257	0.5067	0.0775	-0.0422	0.2613	0.0063	0.319	29.133	20.9657	34.8441
34	0.8208	-0.467	0.2326	3.6119	0.3183	2.3038	-0.0926	-0.0925	0.204	0.5889	-0.0283	0.4401	-0.4958	-0.3001	0.1285	0.65	0.1357	0.098	0.4003	-0.0752	0.4313	17.8831	22.1141	51.9561

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 2 through 53 )	A	2 - 53
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 54 through 69 )	A	54 - 69
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 70 through 88 )	A	70 - 88
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 89 through 122 )	A	89 - 122
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 123 through 197 )	A	123 - 197
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 198 through 216 )	A	198 - 216
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 217 through 238 )	A	217 - 238
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 239 through 282 )	A	239 - 282
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 283 through 304 )	A	283 - 304
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 53 )	B	2 - 53
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 54 through 69 )	B	54 - 69
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 70 through 88 )	B	70 - 88
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 89 through 122 )	B	89 - 122
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 123 through 197 )	B	123 - 197
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 198 through 216 )	B	198 - 216
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 217 through 238 )	B	217 - 238
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 239 through 304 )	B	239 - 304
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 2 through 53 )	C	2 - 53
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 54 through 69 )	C	54 - 69
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 70 through 88 )	C	70 - 88
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 89 through 122 )	C	89 - 122
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 123 through 197 )	C	123 - 197
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 198 through 216 )	C	198 - 216
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 217 through 238 )	C	217 - 238
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 239 through 282 )	C	239 - 282
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 283 through 304 )	C	283 - 304
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 2 through 53 )	D	2 - 53
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 54 through 69 )	D	54 - 69
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 70 through 88 )	D	70 - 88
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 89 through 122 )	D	89 - 122
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 123 through 197 )	D	123 - 197
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 198 through 216 )	D	198 - 216
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 217 through 238 )	D	217 - 238
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 239 through 304 )	D	239 - 304

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