PDB-6h9s: Crystal dimeric structure of Petrotoga mobilis lactate dehydrogen...

ID or keywords:

Entry

Database: PDB / ID: 6h9s

Title

Crystal dimeric structure of Petrotoga mobilis lactate dehydrogenase with NADH

Components

L-lactate dehydrogenase

Keywords

OXIDOREDUCTASE / Petrotoga mobilis / Lactate dehydrogenase / NADH

Function / homology

Function and homology information

L-lactate dehydrogenase / L-lactate dehydrogenase activity / glycolytic process / cytoplasm
Similarity search - Function

Biological species

Petrotoga mobilis

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Roche, J. / Engilberge, S. / Girard, E. / Madern, D.

Funding support

France, 1items

Citation

Journal: To Be Published
Title: Structure of Petrotoga mobilis lactate dehydrogenase at 1.9 Angstrom resolution
Authors: Roche, J. / Engilberge, S. / Girard, E. / Madern, D.

History

Deposition	Aug 6, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 22, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	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

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Download

PDBx/mmCIF format	6h9s.cif.gz	243.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6h9s.ent.gz	198.2 KB	Display	PDB format
PDBx/mmJSON format	6h9s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6h9s_validation.pdf.gz	998 KB	Display	wwPDB validaton report
Full document	6h9s_full_validation.pdf.gz	1003.6 KB	Display
Data in XML	6h9s_validation.xml.gz	24.4 KB	Display
Data in CIF	6h9s_validation.cif.gz	34.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h9/6h9s ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h9s	HTTPS FTP

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Related structure data

Related structure data	1a5zS S: Starting model for refinement
Similar structure data	1lth-1 1lld-1 5dnd-d 1a5z-1 5dnc-d 5dne-d 4r8l-d 2e37-6 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	#102 - Jun 2008 Lactate Dehydrogenase similarity (11) #154 - Oct 2012 Citric Acid Cycle similarity (6) #142 - Oct 2011 PDB Pioneers similarity (10)

Deposited unit

A: L-lactate dehydrogenase

B: L-lactate dehydrogenase

hetero molecules

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

1

A: L-lactate dehydrogenase

B: L-lactate dehydrogenase

hetero molecules

A: L-lactate dehydrogenase

B: L-lactate dehydrogenase

hetero molecules

defined by software
Evidence: gel filtration
136 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	91.268, 103.739, 90.700
Angle α, β, γ (deg.)	90.00, 107.25, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	L-lactate dehydrogenase / L-LDH Mass: 33384.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Petrotoga mobilis (strain DSM 10674 / SJ95) (bacteria) Strain: DSM 10674 / SJ95 / Gene: ldh, Pmob_1893 / Production host: Escherichia coli (E. coli) / References: UniProt: A9BGZ9, L-lactate dehydrogenase
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.07 Å³/Da / Density % sol: 59.95 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 20%, NaNO3 0.1 M

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 19, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.966 Å / Relative weight: 1
Reflection	Resolution: 1.9→44.51 Å / Num. obs: 62820 / % possible obs: 99 % / Redundancy: 1.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.027 / R_rim(I) all: 0.039 / Net I/σ(I): 2.3
Reflection shell	Resolution: 1.9→1.97 Å / R_merge(I) obs: 0.357 / Num. unique all: 6301 / CC_1/2: 0.749

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1A5Z

1a5z

Resolution: 1.9→44.501 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.84 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1969	3243	5.16 %
R_work	0.1693	-	-
obs	0.1707	62809	98.93 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→44.501 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4413	0	88	196	4697

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4647
X-RAY DIFFRACTION	f_angle_d	0.774	6313
X-RAY DIFFRACTION	f_dihedral_angle_d	14.298	2793
X-RAY DIFFRACTION	f_chiral_restr	0.056	758
X-RAY DIFFRACTION	f_plane_restr	0.005	781

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 (%)
1.9-1.9284	0.3491	119	0.2954	2630	X-RAY DIFFRACTION	99
1.9284-1.9585	0.2815	136	0.2587	2542	X-RAY DIFFRACTION	99
1.9585-1.9906	0.2463	138	0.2289	2608	X-RAY DIFFRACTION	99
1.9906-2.0249	0.2573	148	0.209	2590	X-RAY DIFFRACTION	99
2.0249-2.0617	0.242	148	0.1953	2586	X-RAY DIFFRACTION	100
2.0617-2.1014	0.2343	137	0.187	2589	X-RAY DIFFRACTION	99
2.1014-2.1443	0.2024	152	0.1817	2581	X-RAY DIFFRACTION	100
2.1443-2.1909	0.2048	139	0.1752	2609	X-RAY DIFFRACTION	100
2.1909-2.2419	0.2126	144	0.1753	2578	X-RAY DIFFRACTION	99
2.2419-2.2979	0.217	151	0.1645	2619	X-RAY DIFFRACTION	99
2.2979-2.3601	0.2053	136	0.174	2561	X-RAY DIFFRACTION	99
2.3601-2.4295	0.235	131	0.1795	2591	X-RAY DIFFRACTION	99
2.4295-2.5079	0.1992	158	0.1704	2593	X-RAY DIFFRACTION	100
2.5079-2.5976	0.2132	132	0.1684	2610	X-RAY DIFFRACTION	99
2.5976-2.7015	0.1809	152	0.166	2583	X-RAY DIFFRACTION	99
2.7015-2.8245	0.193	119	0.1763	2611	X-RAY DIFFRACTION	99
2.8245-2.9734	0.2382	152	0.1829	2552	X-RAY DIFFRACTION	99
2.9734-3.1596	0.2245	178	0.1841	2558	X-RAY DIFFRACTION	99
3.1596-3.4035	0.1945	134	0.1702	2589	X-RAY DIFFRACTION	99
3.4035-3.7458	0.1771	146	0.1571	2586	X-RAY DIFFRACTION	98
3.7458-4.2875	0.1516	125	0.1433	2614	X-RAY DIFFRACTION	98
4.2875-5.4003	0.1627	133	0.1404	2593	X-RAY DIFFRACTION	98
5.4003-44.513	0.1747	135	0.1659	2593	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	2.4829	0.6457	-0.7247	6.0582	-1.162	4.8533	-0.1102	-0.1268	-0.0406	0.2696	-0.0393	-0.1533	-0.2741	0.0424	0.1629	0.1742	0.0357	-0.0603	0.1936	-0.0113	0.1828	12.4843	25.8997	-10.3109
2	6.7107	1.3375	-0.8047	4.3434	3.951	4.3658	0.0616	0.0098	0.0256	-0.0569	0.2567	-0.9964	-0.1718	0.3088	-0.4004	0.2763	0.0343	0.0381	0.2766	-0.0319	0.4099	25.6389	21.5535	-15.0977
3	1.6622	0.9789	0.0203	3.3961	2.3602	2.5409	0.087	-0.0065	-0.0592	0.1574	0.0272	-0.383	0.0449	0.039	-0.0862	0.2664	0.0195	-0.0161	0.2043	0.0348	0.2455	17.4925	24.002	-4.9516
4	4.5051	0.539	-2.3073	3.4434	-0.4228	7.9811	0.1689	0.4529	-0.0773	-0.4322	-0.116	-0.1314	-0.593	0.4088	-0.0654	0.2729	0.0053	0.0008	0.2822	-0.0429	0.1897	14.9706	20.4518	-26.6309
5	2.8431	-0.5105	0.144	5.3644	-0.7194	4.5945	0.0627	0.333	-0.3513	-0.1437	-0.0842	0.0818	0.3153	-0.1685	0.0099	0.282	0.0075	0.0082	0.2652	-0.087	0.2337	7.1401	15.5258	-24.1113
6	7.6434	-5.8321	-1.3527	4.6256	1.2268	2.3704	0.061	0.3106	0.3082	0.0183	0.0571	-0.1942	0.0453	-0.1161	-0.1102	0.2195	-0.0028	-0.0143	0.2851	0.0384	0.2074	-1.1901	38.3503	-23.3257
7	9.4647	3.3351	0.5876	8.8852	-3.247	9.8477	-0.1778	0.6851	0.4822	0.3271	0.2504	0.2022	-0.3736	-0.2081	-0.0731	0.276	0.0792	0.0386	0.3487	0.0241	0.3298	-8.8922	45.4443	-18.6141
8	6.018	-4.3408	0.5775	6.9446	1.3479	5.4964	0.0928	0.6472	-0.0257	-0.2804	-0.4069	0.209	-0.0656	0.0167	0.2656	0.2949	0.0132	-0.0291	0.4126	0.0356	0.2492	-5.5196	35.5113	-30.489
9	6.0005	-0.3298	0.0652	2.1326	-0.683	3.3971	0.33	1.1261	0.9227	-0.4272	-0.0721	0.2861	-0.4461	-0.4919	-0.3164	0.3956	0.0295	-0.046	0.5212	0.1431	0.4061	-7.3241	45.1236	-29.1014
10	2.4846	2.3519	1.0394	2.4342	1.5354	9.7129	-0.1595	1.1658	0.2772	-0.901	0.3699	-0.6813	-0.2911	0.4256	-0.1979	0.4138	0.0013	0.0852	0.5734	-0.0056	0.4314	15.013	41.2104	-27.519
11	4.3104	5.4346	-0.7876	7.2828	-0.5079	1.6977	0.0735	-0.2251	0.1378	0.2777	-0.0878	-0.0557	-0.0534	-0.1098	-0.0525	0.212	0.0426	-0.0201	0.2422	-0.0024	0.2063	1.7022	28.9516	-14.1428
12	1.8495	0.1799	0.0073	6.6499	-0.0318	4.7311	0.0378	0.5993	-0.3624	-0.3648	0.0239	0.4929	0.2006	-0.4629	-0.0811	0.2246	-0.0012	-0.0566	0.3975	-0.0842	0.2542	-5.4396	22.4193	-25.4748
13	5.8662	-4.1428	0.0953	4.3347	-0.4027	0.0655	0.7213	1.4596	-0.2391	-1.2137	-0.7883	0.256	-0.1599	-0.2601	-0.0033	0.6192	0.099	-0.0393	0.8398	-0.0602	0.2933	-1.6029	27.1004	-40.1418
14	4.1224	0.1041	-0.4477	6.3672	0.3264	3.5206	0.0195	0.1419	0.0561	-0.3906	0.078	0.4764	-0.0104	-0.2533	-0.0997	0.2128	-0.0154	-0.0868	0.1743	0.0448	0.1787	13.6301	46.5167	-9.5344
15	7.9136	7.1664	-0.7034	8.4852	0.1625	1.7926	-0.408	0.5485	0.1374	-0.6908	0.2169	-0.0215	-0.1913	0.0798	0.1432	0.3091	0.0077	-0.0336	0.2619	0.076	0.2348	13.9095	45.7106	-18.8239
16	1.5067	0.0486	1.7778	3.2935	1.3036	2.5526	-0.2024	0.1231	0.5394	-0.3692	-0.0366	0.2553	-0.3876	-0.0777	0.1973	0.2728	0.0118	-0.0707	0.2156	0.0749	0.3412	13.6058	53.9854	-11.0274
17	9.4313	-3.575	1.5199	6.5779	-0.2241	2.3209	0.038	0.3841	-0.732	-0.3278	0.01	-0.1755	-0.0727	0.3877	-0.043	0.2662	-0.0583	0.0354	0.2685	0.0105	0.3762	33.6556	52.817	-7.4668
18	1.0257	1.1134	-0.5142	3.0424	-0.465	0.9228	0.0441	-0.107	0.0634	0.0271	-0.0395	-0.2092	-0.0747	0.0659	-0.0025	0.2005	-0.016	-0.02	0.2056	-0.0071	0.285	24.797	52.6935	1.6155
19	5.8147	3.8432	-2.6604	2.7915	-1.5109	5.8324	-0.1929	-0.3354	-0.176	0.1167	0.0892	0.4802	0.4333	-0.273	0.0906	0.2504	0.0138	-0.016	0.2703	0.0468	0.2719	18.1572	29.0738	12.2695
20	5.5806	4.0256	0.2691	9.074	-5.3234	5.4246	0.1221	-0.0738	-0.146	0.1655	-0.302	-0.4148	-0.0423	0.148	0.31	0.2673	0.0206	-0.0693	0.2927	0.0205	0.2751	27.6785	36.1629	13.9731
21	1.8527	2.7462	-0.8644	4.6972	0.8683	7.5142	0.6642	-0.4976	-0.9214	0.2372	-0.3715	-0.5039	1.3421	0.0536	-0.3284	0.4966	0.0947	-0.0988	0.5852	0.1303	0.5082	23.6655	25.6409	20.7118
22	7.1815	0.9439	-3.57	2.2181	-1.6393	2.7127	-0.3484	-0.1033	-0.1413	-0.1633	-0.0683	-0.6012	0.5849	1.2022	0.4007	0.3132	0.0325	0.0211	0.3666	0.0218	0.4447	31.4219	29.3714	1.6493
23	5.7107	-3.2942	-3.5221	3.7467	3.5776	4.6403	-0.2237	-0.0324	-0.1165	-0.1161	0.1739	-0.0721	0.0723	0.0695	0.0617	0.2643	-0.0149	-0.0012	0.2056	0.0207	0.2483	18.6024	39.5858	-3.0849
24	2.4334	-1.0776	-0.7846	5.3007	-1.3338	3.0225	0.1122	-0.3752	0.0735	0.3053	-0.1029	0.2014	-0.1925	-0.0743	-0.0096	0.223	-0.0362	-0.0244	0.2285	-0.021	0.222	20.6104	48.9661	11.6592
25	1.3762	2.9426	-1.728	7.5166	-4.4684	2.6605	0.0912	-0.5876	-0.5656	0.6881	-0.6082	-1.375	0.1288	0.5261	0.5477	0.3898	-0.0458	-0.1802	0.4949	0.0898	0.4941	35.8628	40.0947	19.1913
26	7.7405	1.932	-1.6978	8.4929	-5.1402	3.809	-0.0973	-0.318	0.2585	-0.0544	-0.1283	-0.9903	-0.2657	0.5421	0.271	0.2399	-0.0183	-0.0018	0.3357	-0.0105	0.5834	40.5337	51.6728	5.0798

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:30)
2	X-RAY DIFFRACTION	2	(chain A and resid 31:39)
3	X-RAY DIFFRACTION	3	(chain A and resid 40:65)
4	X-RAY DIFFRACTION	4	(chain A and resid 66:100)
5	X-RAY DIFFRACTION	5	(chain A and resid 101:139)
6	X-RAY DIFFRACTION	6	(chain A and resid 140:154)
7	X-RAY DIFFRACTION	7	(chain A and resid 155:164)
8	X-RAY DIFFRACTION	8	(chain A and resid 165:184)
9	X-RAY DIFFRACTION	9	(chain A and resid 185:216)
10	X-RAY DIFFRACTION	10	(chain A and resid 217:228)
11	X-RAY DIFFRACTION	11	(chain A and resid 229:250)
12	X-RAY DIFFRACTION	12	(chain A and resid 251:279)
13	X-RAY DIFFRACTION	13	(chain A and resid 280:303)
14	X-RAY DIFFRACTION	14	(chain B and resid 1:30)
15	X-RAY DIFFRACTION	15	(chain B and resid 31:52)
16	X-RAY DIFFRACTION	16	(chain B and resid 53:75)
17	X-RAY DIFFRACTION	17	(chain B and resid 76:105)
18	X-RAY DIFFRACTION	18	(chain B and resid 106:147)
19	X-RAY DIFFRACTION	19	(chain B and resid 148:165)
20	X-RAY DIFFRACTION	20	(chain B and resid 166:187)
21	X-RAY DIFFRACTION	21	(chain B and resid 188:208)
22	X-RAY DIFFRACTION	22	(chain B and resid 209:223)
23	X-RAY DIFFRACTION	23	(chain B and resid 224:244)
24	X-RAY DIFFRACTION	24	(chain B and resid 245:279)
25	X-RAY DIFFRACTION	25	(chain B and resid 280:291)
26	X-RAY DIFFRACTION	26	(chain B and resid 292:305)

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