PDB-8q3c: Structure of Selenomonas ruminantium lactate dehydrogenase I85R mutant

ID or keywords:

Entry

Database: PDB / ID: 8q3c

Title

Structure of Selenomonas ruminantium lactate dehydrogenase I85R mutant

Components

(L-lactate dehydrogenase) x 2

Keywords

OXIDOREDUCTASE / Allosteric regulation / lactate dehydrogenase / mutant

Function / homology

Function and homology information

L-lactate dehydrogenase / L-lactate dehydrogenase activity / carboxylic acid metabolic process / carbohydrate metabolic process / cytoplasm
Similarity search - Function

Biological species

Selenomonas ruminantium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Bertrand, Q. / Coquille, S. / Iorio, A. / Sterpone, F. / Madern, D.

Funding support

France, 1items

Citation

Journal: J.Struct.Biol. / Year: 2023
Title: Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete ...
Authors: Bertrand, Q. / Coquille, S. / Iorio, A. / Sterpone, F. / Madern, D.

History

Deposition	Aug 3, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 1, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Database references / Category: citation Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 15, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8q3c.cif.gz	626.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8q3c.ent.gz	530 KB	Display	PDB format
PDBx/mmJSON format	8q3c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8q3c_validation.pdf.gz	479.9 KB	Display	wwPDB validaton report
Full document	8q3c_full_validation.pdf.gz	487.1 KB	Display
Data in XML	8q3c_validation.xml.gz	39 KB	Display
Data in CIF	8q3c_validation.cif.gz	53.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q3/8q3c ftp://data.pdbj.org/pub/pdb/validation_reports/q3/8q3c	HTTPS FTP

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Related structure data

Related structure data	7nayC C: citing same article (ref.)
Similar structure data	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 (9) #154 - Oct 2012 Citric Acid Cycle similarity (6) #142 - Oct 2011 PDB Pioneers similarity (8)

Deposited unit

H: L-lactate dehydrogenase

N: L-lactate dehydrogenase

U: L-lactate dehydrogenase

a: L-lactate dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry, gel filtration

Unit cell

Length a, b, c (Å)	72.290, 129.660, 133.410
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 2 types, 4 molecules HNaU

#1: Protein	L-lactate dehydrogenase Mass: 35061.012 Da / Num. of mol.: 3 / Mutation: I85R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Gene: ldh / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EVR0
#2: Protein	L-lactate dehydrogenase Mass: 35141.012 Da / Num. of mol.: 1 / Mutation: I85R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Gene: ldh / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EVR0

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Non-polymers , 4 types, 16 molecules

#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO₃
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.82 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M BisTris propane pH 7.5, 0.2 M NaNO3, 16 to 26 % PEG 3,350 (optimized from Molecular Dimensions PACT screen, condition 77).

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.979507 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979507 Å / Relative weight: 1
Reflection	Resolution: 2.78→19.81 Å / Num. obs: 60734 / % possible obs: 99.5 % / Redundancy: 7.05 % / CC_1/2: 0.99 / R_pim(I) all: 0.035 / R_rim(I) all: 0.14 / Net I/σ(I): 10.12
Reflection shell	Resolution: 2.78→2.85 Å / Redundancy: 6.35 % / Mean I/σ(I) obs: 0.36 / Num. unique obs: 4430 / CC_1/2: 0.117 / R_pim(I) all: 0.619 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.1→19.81 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2875	2175	4.98 %
R_work	0.2581	-	-
obs	0.2596	43700	99.86 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.1→19.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8573	0	18	11	8602

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8704
X-RAY DIFFRACTION	f_angle_d	0.434	11805
X-RAY DIFFRACTION	f_dihedral_angle_d	12.671	3040
X-RAY DIFFRACTION	f_chiral_restr	0.042	1421
X-RAY DIFFRACTION	f_plane_restr	0.004	1510

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 (%)
3.1-3.17	0.4109	140	0.3702	2588	X-RAY DIFFRACTION	100
3.17-3.24	0.3531	137	0.3531	2592	X-RAY DIFFRACTION	100
3.24-3.32	0.3272	140	0.329	2612	X-RAY DIFFRACTION	100
3.32-3.41	0.3965	130	0.3238	2568	X-RAY DIFFRACTION	100
3.41-3.51	0.3177	140	0.3238	2618	X-RAY DIFFRACTION	100
3.51-3.62	0.3292	138	0.3088	2607	X-RAY DIFFRACTION	100
3.62-3.75	0.3341	134	0.2972	2544	X-RAY DIFFRACTION	100
3.75-3.9	0.3103	135	0.285	2627	X-RAY DIFFRACTION	100
3.9-4.08	0.2807	138	0.2668	2606	X-RAY DIFFRACTION	100
4.08-4.29	0.2776	133	0.2353	2586	X-RAY DIFFRACTION	100
4.29-4.56	0.2519	132	0.2383	2596	X-RAY DIFFRACTION	100
4.56-4.9	0.2695	141	0.2339	2609	X-RAY DIFFRACTION	100
4.9-5.39	0.2608	130	0.2469	2591	X-RAY DIFFRACTION	100
5.39-6.15	0.2711	138	0.2809	2605	X-RAY DIFFRACTION	100
6.15-7.67	0.3293	133	0.2652	2588	X-RAY DIFFRACTION	100
7.67-19.81	0.2449	136	0.1966	2588	X-RAY DIFFRACTION	99

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	2.1147	0.1993	0.8857	1.5286	1.6907	1.9332	0.4418	0.7226	-0.4815	-0.1072	-0.431	0.6645	0.3092	0.0099	0.0013	0.7723	-0.0454	-0.31	0.985	0.026	0.8087	-42.946	0.922	-10.781
2	0.3303	-0.3188	0.2645	0.7033	0.3342	0.8123	0.1833	0.0085	0.2792	-0.6139	-0.4997	0.8377	-1.0329	-0.1027	0	0.9186	0.1538	-0.2085	0.9882	0.0615	1.0715	-43.296	17.792	-18.743
3	0.7465	0.9354	0.9427	1.3064	0.5963	2.6063	0.2672	-0.081	0.3822	-0.5689	0.1209	-0.2259	-0.1403	0.0639	-0.0002	0.8826	0.1268	0.2167	0.7874	0.0039	0.8229	-12.927	15.78	-17.775
4	0.0792	0.0665	0.0413	0.2859	0.2532	0.1698	0.4818	1.6706	0.7662	-0.0695	-0.1497	1.082	0.1479	1.1284	0.0003	1.337	0.2959	0.1169	1.7096	0.0285	0.9002	-18.66	11.434	-29.001
5	3.0532	-0.309	0.0117	0.9504	-0.7174	0.4303	0.0907	0.373	0.75	-0.3297	-0.0701	-0.1503	-0.1399	-0.2784	0	0.6765	-0.0206	-0.045	0.8694	0.1309	0.8051	-30.189	20.898	-12.914
6	0.3556	-0.6008	-0.4519	1.0558	0.876	0.7862	1.0299	-0.6583	0.0253	-0.479	-0.3094	-0.0162	-0.1492	-0.151	-0.0005	1.5393	-0.065	0.035	1.4278	0.4652	1.079	-29.38	28.605	-28.545
7	0.3372	0.8912	0.0544	1.6766	-0.1273	0.2313	0.3796	-0.1157	-0.5514	0.2452	-0.1404	-0.5322	0.6734	0.0839	-0	0.9987	-0.0084	-0.4314	0.7406	0.0416	0.9045	-8.621	-4.397	10.893
8	0.9065	0.6981	-0.2897	3.2557	-0.8845	2.3976	0.228	0.1589	0.4967	-0.1606	0.0407	-0.5564	-0.1001	0.2317	-0.0001	0.5364	-0.042	0.0187	0.7551	-0.101	0.997	-15.218	24.458	4.789
9	1.9134	0.5849	-0.6924	3.2839	-1.6943	0.8844	0.3805	-0.0327	0.334	0.284	-0.1794	-0.5874	0.1297	0.3611	0	0.6396	0.0775	-0.0772	0.7714	-0.062	1.0381	-2.416	12.296	2.808
10	-0.0867	-0.0438	0.3829	1.5336	0.316	2.469	0.2529	-0.4809	0.2207	0.2138	-0.0037	-0.0457	0.2465	-0.0191	0.002	0.6974	-0.1974	-0.0126	0.9195	-0.0521	0.551	-32.657	11.675	15.688
11	0.4173	-0.3036	-0.4264	0.8936	0.458	0.4009	-0.0249	-0.4262	0.1731	0.4812	-0.7389	-0.2696	0.3208	-0.3413	-0.0001	1.2265	-0.4645	0.124	1.4326	0.0116	0.8089	-45.622	4.754	21.939
12	0.7417	0.1482	-0.7568	0.1171	-0.1481	0.7115	0.6695	-0.3572	-0.9176	-0.0301	-0.5008	0.4541	0.6407	-0.7603	0	1.3022	-0.5041	-0.299	1.1417	0.347	1.0687	-32.511	-16.86	14.379
13	2.3406	-1.3743	-0.377	2.7729	-0.6388	0.2379	-0.1622	-0.2618	-0.5544	-0.1739	0.2731	0.4102	0.806	-0.5051	0.0004	1.2693	-0.4553	-0.0692	0.9711	0.1233	0.8595	-39.358	-11.709	17.789
14	1.2415	0.2356	1.7362	0.491	-0.0501	2.2401	0.4723	0.2341	-0.3196	-0.2799	0.1619	-0.2975	0.7791	0.6281	0.0141	1.2687	0.1591	-0.1568	0.8868	-0.2653	0.7423	-20.342	-8.458	-18.331
15	0.685	0.5573	-0.1628	0.8762	-0.7454	0.6461	0.8882	-0.2608	-1.1831	-0.249	0.4426	0.297	1.0221	-0.4864	0.8911	1.1803	-0.4296	-0.8679	0.2777	-0.5288	0.9705	-33.908	-20.421	-10.202
16	2.4634	-1.4897	-0.0651	1.3474	0.1895	0.07	1.1332	0.435	-1.1552	-0.1705	-0.8667	0.5835	-0.219	-0.5614	0.0036	1.4019	-0.2028	-0.5401	1.1134	0.0507	1.1689	-49.635	-19.278	-6.435
17	1.3583	1.2574	-0.0914	1.8658	0.2129	0.2017	0.5483	0.2689	-1.1083	0.7016	-0.0732	-0.0435	0.2851	-0.0728	0.0127	1.1426	-0.0341	-0.5554	0.8383	-0.1012	1.2858	-31.153	-24.101	-8.359

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN H AND RESID 2:73 )	H	2 - 73
2	X-RAY DIFFRACTION	2	( CHAIN H AND RESID 74:148 )	H	74 - 148
3	X-RAY DIFFRACTION	3	( CHAIN H AND RESID 149:212 )	H	149 - 212
4	X-RAY DIFFRACTION	4	( CHAIN H AND RESID 213:230 )	H	213 - 230
5	X-RAY DIFFRACTION	5	( CHAIN H AND RESID 231:294 )	H	231 - 294
6	X-RAY DIFFRACTION	6	( CHAIN H AND RESID 295:317 )	H	295 - 317
7	X-RAY DIFFRACTION	7	( CHAIN N AND RESID 1:148 )	N	1 - 148
8	X-RAY DIFFRACTION	8	( CHAIN N AND RESID 149:230 )	N	149 - 230
9	X-RAY DIFFRACTION	9	( CHAIN N AND RESID 231:315 )	N	231 - 315
10	X-RAY DIFFRACTION	10	( CHAIN U AND RESID 1:112 )	U	1 - 112
11	X-RAY DIFFRACTION	11	( CHAIN U AND RESID 113:148 )	U	113 - 148
12	X-RAY DIFFRACTION	12	( CHAIN U AND RESID 149:187 )	U	149 - 187
13	X-RAY DIFFRACTION	13	( CHAIN U AND RESID 188:315 )	U	188 - 315
14	X-RAY DIFFRACTION	14	( CHAIN a AND RESID 2:114 )	a	2 - 114
15	X-RAY DIFFRACTION	15	( CHAIN a AND RESID 115:185 )	a	115 - 185
16	X-RAY DIFFRACTION	16	( CHAIN a AND RESID 186:231 )	a	186 - 231
17	X-RAY DIFFRACTION	17	( CHAIN a AND RESID 232:314 )	a	232 - 314

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