PDB-4a73: SINGLE POINT MUTANT OF THERMUS THERMOPHILUS LACTATE DEHYDROGENASE

ID or keywords:

Entry

Database: PDB / ID: 4a73

Title

SINGLE POINT MUTANT OF THERMUS THERMOPHILUS LACTATE DEHYDROGENASE

Components

L-LACTATE DEHYDROGENASE

Keywords

OXIDOREDUCTASE / THERMOPHILE

Function / homology

Function and homology information

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

Biological species

THERMUS THERMOPHILUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.001 Å

Authors

De Mendoza-Barbera, E. / Vellieux, F.M.D.

Citation

Journal: Mol.Biol.Evol. / Year: 2012
Title: Sampling the Conformational Energy Landscape of a Hyperthermophilic Protein by Engineering Key Substitutions
Authors: Colletier, J.P. / Aleksandrov, A. / Coquelle, N. / Mraihi, S. / De Mendoza-Barbera, E. / Field, M. / Madern, D.

History

Deposition	Nov 10, 2011	Deposition site: PDBE / Processing site: PDBE
Supersession	Dec 28, 2011	ID: 2XXE
Revision 1.0	Dec 28, 2011	Provider: repository / Type: Initial release
Revision 1.1	Feb 1, 2012	Group: Other
Revision 1.2	Apr 18, 2012	Group: Other
Revision 1.3	May 30, 2012	Group: Other
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4a73.cif.gz	478.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4a73.ent.gz	403 KB	Display	PDB format
PDBx/mmJSON format	4a73.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4a73_validation.pdf.gz	449.6 KB	Display	wwPDB validaton report
Full document	4a73_full_validation.pdf.gz	474.2 KB	Display
Data in XML	4a73_validation.xml.gz	45.4 KB	Display
Data in CIF	4a73_validation.cif.gz	63.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a7/4a73 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/4a73	HTTPS FTP

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Related structure data

Related structure data	3zznC 2v6mS 2v7p 2xxb 2xxj C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3zzn-d 2v6m-d 2q08-3 4i9q-2 3vpg-d 2e37-6 2qee-4 2e37-1 3qep-d 3spz-d 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 (10) #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

C: L-LACTATE DEHYDROGENASE

D: L-LACTATE DEHYDROGENASE

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	158.040, 158.040, 142.110
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	L-LACTATE DEHYDROGENASE / L-LDH Mass: 32744.463 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PTTHLDH12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] / References: UniProt: Q5SJA1, L-lactate dehydrogenase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, ARG 199 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 199 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ARG 199 TO ALA ENGINEERED RESIDUE IN CHAIN B, ARG 199 TO ALA ENGINEERED RESIDUE IN CHAIN C, ARG 199 TO ALA ENGINEERED RESIDUE IN CHAIN D, ARG 199 TO ALA

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.6 Å³/Da / Density % sol: 65.88 % / Description: NONE
Crystal grow	pH: 6 Details: 2.4 M NAFORMATE, 0.1 M MES PH 6.0. DROPLETS ARE 2 MICROL PROTEIN PLUS 2 MICROL PRECIPITANT

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97245
Detector	Type: ADSC CCD / Detector: CCD / Date: Jan 31, 2010 / Details: MIRRORS
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97245 Å / Relative weight: 1
Reflection	Resolution: 3→136.87 Å / Num. obs: 39979 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.23 % / B_iso Wilson estimate: 80.33 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 19.96
Reflection shell	Resolution: 3→3.18 Å / Redundancy: 3.24 % / R_merge(I) obs: 0.63 / Mean I/σ(I) obs: 2.22 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.7.2_869)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V6M

2v6m

Resolution: 3.001→49.29 Å / SU ML: 0.81 / σ(F): 1.99 / Phase error: 25.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2346	1998	5 %
R_work	0.1695	-	-
obs	0.1727	39965	99.12 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 68.493 Å² / k_sol: 0.331 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	6.8392 Å²	0 Å²	0 Å²
2-	-	6.8392 Å²	0 Å²
3-	-	-	-13.6783 Å²

Refinement step

Cycle: LAST / Resolution: 3.001→49.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9219	0	0	171	9390

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	9437
X-RAY DIFFRACTION	f_angle_d	1.265	12855
X-RAY DIFFRACTION	f_dihedral_angle_d	17.934	3435
X-RAY DIFFRACTION	f_chiral_restr	0.078	1508
X-RAY DIFFRACTION	f_plane_restr	0.005	1686

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 (%)
3.0012-3.0762	0.3359	140	0.2728	2661	X-RAY DIFFRACTION	98
3.0762-3.1594	0.4002	143	0.2797	2721	X-RAY DIFFRACTION	99
3.1594-3.2523	0.3882	141	0.2837	2675	X-RAY DIFFRACTION	100
3.2523-3.3573	0.3654	143	0.2506	2715	X-RAY DIFFRACTION	99
3.3573-3.4772	0.2872	142	0.2225	2701	X-RAY DIFFRACTION	99
3.4772-3.6164	0.2808	143	0.1971	2723	X-RAY DIFFRACTION	100
3.6164-3.781	0.2393	142	0.1813	2705	X-RAY DIFFRACTION	99
3.781-3.9802	0.263	144	0.1564	2725	X-RAY DIFFRACTION	100
3.9802-4.2295	0.1856	143	0.1365	2719	X-RAY DIFFRACTION	100
4.2295-4.5558	0.1999	144	0.1164	2733	X-RAY DIFFRACTION	100
4.5558-5.0139	0.1757	142	0.1215	2708	X-RAY DIFFRACTION	100
5.0139-5.7385	0.2095	145	0.1486	2739	X-RAY DIFFRACTION	99
5.7385-7.2262	0.2305	143	0.1752	2727	X-RAY DIFFRACTION	99
7.2262-49.2971	0.1925	143	0.1575	2715	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	1.4238	0.5323	-0.1976	2.0999	-0.7465	5.5419	0.2728	-0.3974	0.2969	0.4575	-0.3149	0.0377	-0.4529	-0.5638	0.1081	0.4828	-0.0362	-0.0773	0.5264	-0.2074	0.5105	49.4314	-42.3578	12.163
2	6.9963	3.4818	5.9652	7.8125	0.5369	8.1941	0.296	-0.7281	-0.0068	0.0844	-0.2994	0.407	0.9773	0.0323	-0.0522	0.5727	0.0162	0.132	0.6942	0.0114	0.4354	49.0653	-71.7755	4.7032
3	1.5974	-0.1412	-0.2247	3.2708	-0.0479	3.1725	-0.2383	-0.4484	-0.2429	0.4327	0.095	0.0991	-0.0973	-0.0575	0.1262	0.3895	0.0394	-0.0358	0.5043	-0.1064	0.3246	49.811	-60.9821	10.6141
4	4.9559	2.4731	1.7636	4.4415	5.0705	8.0493	0.0666	-1.1647	-0.6978	0.1095	0.3576	-0.4248	0.5243	-0.3023	-0.4167	0.7536	0.0422	-0.1309	0.8458	0.1859	0.3121	51.737	-66.6043	23.8426
5	1.65	-0.2045	-1.1982	1.7537	-2.4658	4.7446	-0.2349	0.1386	-0.5364	-0.3157	-0.3581	-0.777	0.2772	-0.1874	0.489	0.3704	0.0977	0.0284	0.274	-0.1134	0.591	62.6228	-50.2628	-11.5792
6	3.0852	-1.0154	-0.338	3.3167	-0.1221	1.9932	-0.3425	0.5404	0.4654	-0.2082	-0.2726	0.1572	-0.3352	-0.0363	0.5612	0.5175	-0.1455	-0.1192	0.3963	-0.0612	0.7388	52.3011	-33.3779	-20.2209
7	0.4758	-0.0145	-0.2377	2.5736	0.1622	0.7508	0.2973	0.0113	-0.0931	0.0374	0.1082	0.1553	-0.0163	0.111	0.869	1.0024	-0.1064	-0.3137	-0.1907	-0.4765	1.0093	47.7593	-18.3303	-10.8115
8	2.2082	0.3472	-0.1737	3.3063	0.3155	3.0563	-0.5051	0.2782	0.5298	-0.8096	-0.1002	0.1807	-0.6422	0.2394	0.4049	0.4696	-0.1067	-0.0811	0.349	-0.0063	0.7255	56.414	-32.6847	-22.8256
9	2.6731	-1.0886	-1.2656	5.0353	0.1168	2.2452	-0.0557	-0.7303	0.6123	-0.101	0.4059	0.7944	-0.1119	-1.1866	-0.1699	0.3071	0.0791	0.0382	0.8854	0.014	0.6562	13.1014	-45.2818	-8.9233
10	3.8609	-0.4563	-2.1122	2.5036	-1.3689	4.0043	0.3373	0.3985	1.2182	0.2404	0.3788	0.4443	-0.3392	-0.1202	-0.6378	0.8033	-0.3074	-0.0771	0.4455	0.084	0.8733	31.6977	-36.0247	-30.9593
11	2.4614	0.0219	-0.0226	4.4133	-0.3423	4.6208	0.0459	0.274	0.7812	0.0436	-0.0408	0.6213	-0.7624	-0.1538	-0.0081	0.3458	0.0154	0.006	0.5033	0.1221	0.6475	22.2252	-37.5173	-23.298
12	5.0139	2.2005	-3.1374	1.7896	0.9472	8.6604	0.1897	0.462	0.7937	-0.6601	0.0999	0.1767	-2.0487	-0.4168	-0.1399	0.9573	0.0157	-0.1221	0.646	0.3505	1.4834	14.2748	-25.3848	-27.7665
13	0.3585	-1.0489	0.3532	5.6724	1.0147	3.3451	-0.2935	0.1371	-0.0195	-0.6731	0.3728	0.3511	0.768	-0.0378	-0.0868	0.5531	-0.1188	-0.0076	0.5571	0.0146	0.2626	24.3123	-65.106	-24.7928
14	1.6161	-0.1618	0.2793	0.7068	1.2986	5.0087	0.4356	-0.8176	-0.748	0.1976	0.2491	0.0794	1.1422	0.0294	-0.4516	0.865	-0.0709	-0.0508	0.5638	0.1095	0.4983	28.7497	-74.7742	-5.9189
15	1.9626	0.5984	-2.0487	3.0592	-2.2975	4.8449	0.4465	-1.0955	-0.3497	0.7773	-0.504	0.4757	0.6375	-0.4311	0.0256	0.6443	-0.6788	0.1513	1.1154	0.1694	0.8929	18.2978	-73.705	8.6084
16	2.3378	-0.035	0.0289	1.4513	-0.5833	0.2975	0.0662	-0.2404	-0.9453	0.2222	-0.0095	0.102	1.2525	-0.3179	0.0575	1.2682	-0.2622	-0.0384	0.4512	0.099	0.5474	28.1025	-78.8676	-8.6489

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 22:164)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 165:217)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 218:301)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 302:331)
5	X-RAY DIFFRACTION	5	(CHAIN B AND RESID 22:121)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 122:216)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 217:235)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 236:331)
9	X-RAY DIFFRACTION	9	(CHAIN C AND RESID 22:164)
10	X-RAY DIFFRACTION	10	(CHAIN C AND RESID 165:217)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 218:301)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 302:331)
13	X-RAY DIFFRACTION	13	(CHAIN D AND RESID 22:121)
14	X-RAY DIFFRACTION	14	(CHAIN D AND RESID 122:216)
15	X-RAY DIFFRACTION	15	(CHAIN D AND RESID 217:235)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 236:331)

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