PDB-6or9: Structure of L-lactate dehydrogenase from Trichoplusia ni

ID or keywords:

Entry

Database: PDB / ID: 6or9

Title

Structure of L-lactate dehydrogenase from Trichoplusia ni

Components

L-lactate dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / L-lactate dehydrogenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

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

Trichoplusia ni (cabbage looper)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Structure of L-lactate dehydrogenase from Trichoplusia ni
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Apr 29, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 24, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6or9.cif.gz	489.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6or9.ent.gz	405.4 KB	Display	PDB format
PDBx/mmJSON format	6or9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6or9_validation.pdf.gz	312.1 KB	Display	wwPDB validaton report
Full document	6or9_full_validation.pdf.gz	317.5 KB	Display
Data in XML	6or9_validation.xml.gz	56.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/or/6or9 ftp://data.pdbj.org/pub/pdb/validation_reports/or/6or9	HTTPS FTP

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Related structure data

Similar structure data	3pqe-d 6k12-2 1lld-1 2zqy-d 3usr-2 6dau-d 6k12-1 2p5g-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 (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

159 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)	63.390, 76.480, 79.520
Angle α, β, γ (deg.)	113.06, 109.84, 88.70
Int Tables number	1
Space group name H-M	P1

#1: Protein	L-lactate dehydrogenase Mass: 39737.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichoplusia ni (cabbage looper) / Gene: XP_026745590 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A5H1ZR53*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1097 / 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: 2.08 Å³/Da / Density % sol: 40.92 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MCSG1 H11: 25% (W/V) PEG 3350, 200MM SODIUM CHLORIDE, 100MM HEPES FREE ACID / NAOH PH 7.5: TRNIA.00711.a.GL11.PS38300 AT 14.3 MG/ML + 2MM ATP: CRYO: 15% EG + BSI1767: TRAY 295240 H11: PUCK ...Details: MCSG1 H11: 25% (W/V) PEG 3350, 200MM SODIUM CHLORIDE, 100MM HEPES FREE ACID / NAOH PH 7.5: TRNIA.00711.a.GL11.PS38300 AT 14.3 MG/ML + 2MM ATP: CRYO: 15% EG + BSI1767: TRAY 295240 H11: PUCK DAC0-8 FOR EXPERIMENTAL PHASING, A CRYSTAL FROM THE SAME DROP WAS INCUBATED FOR 15 SEC IN A SOLUTION OF 85% RESERVOIR AND 15% 2.5M SODIUM IODIDE IN ETHYLENE GLYCOL (FINAL IODIDE CONCENTRATION 375MM), AND VITRIFIED IN LIQUID NITROGEN: TRAY 295240H11: PUCK ANX5-15. THE PROTEIN WAS ACCIDENTALLY PURIFIED FROM A CULTURE THAT WAS SUPPOSED TO EXPRESS SSGCID PROTEIN PLFAA.18754.A.GL11., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

Crystal

Density Matthews: 2.08 Å³/Da / Density % sol: 40.92 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MCSG1 H11: 25% (W/V) PEG 3350, 200MM SODIUM CHLORIDE, 100MM HEPES FREE ACID / NAOH PH 7.5: TRNIA.00711.a.GL11.PS38300 AT 14.3 MG/ML + 2MM ATP: CRYO: 15% EG + BSI1767: TRAY 295240 H11: PUCK ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F		1	0.97872
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date
RAYONIX MX-300	1	CCD	Nov 29, 2018
RIGAKU SATURN 944+	2	CCD	Nov 30, 2018

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	C(111)	SINGLE WAVELENGTH	M	x-ray	1
2		SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97872	1
2	1.5418	1

Reflection

Resolution: 1.8→48.906 Å / Num. obs: 115247 / % possible obs: 96.7 % / Redundancy: 2.951 % / B_iso Wilson estimate: 30.18 Å² / R_merge(I) obs: 0.039 / Net I/σ(I): 17.55

Reflection shell

Resolution: 1.8→1.85 Å / Redundancy: 2.68 % / R_merge(I) obs: 0.344 / Mean I/σ(I) obs: 2.74 / % possible all: 93.1

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Processing

Software

Name	Version	Classification
PHENIX		refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
PHASER		phasing
PARROT		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→48.91 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.51

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.195	1971	1.71 %	0
R_work	0.158	-	-	-
obs	0.159	115226	97 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 29.42 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→48.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9055	0	0	1097	10152

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	9457
X-RAY DIFFRACTION	f_angle_d	0.87	12928
X-RAY DIFFRACTION	f_dihedral_angle_d	12.316	5763
X-RAY DIFFRACTION	f_chiral_restr	0.06	1593
X-RAY DIFFRACTION	f_plane_restr	0.005	1637

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 (%)
1.8-1.845	0.313	143	0.2613	7757	X-RAY DIFFRACTION	93
1.845-1.8949	0.2831	138	0.2196	8064	X-RAY DIFFRACTION	96
1.8949-1.9507	0.264	125	0.1943	8006	X-RAY DIFFRACTION	96
1.9507-2.0136	0.197	143	0.1771	8073	X-RAY DIFFRACTION	97
2.0136-2.0856	0.2359	140	0.1746	8075	X-RAY DIFFRACTION	97
2.0856-2.1691	0.2556	137	0.1696	8047	X-RAY DIFFRACTION	97
2.1691-2.2678	0.1902	147	0.1638	8111	X-RAY DIFFRACTION	97
2.2678-2.3874	0.1762	159	0.157	8072	X-RAY DIFFRACTION	97
2.3874-2.537	0.2209	127	0.1572	8151	X-RAY DIFFRACTION	97
2.537-2.7328	0.1753	132	0.1546	8120	X-RAY DIFFRACTION	98
2.7328-3.0078	0.204	158	0.1546	8126	X-RAY DIFFRACTION	98
3.0078-3.443	0.177	127	0.1496	8212	X-RAY DIFFRACTION	98
3.443-4.3373	0.1783	134	0.1358	8255	X-RAY DIFFRACTION	99
4.3373-48.9	0.167	161	0.1483	8186	X-RAY DIFFRACTION	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	2.1247	0.3699	-0.7691	2.3397	-0.2282	4.7861	0.0004	-0.0941	-0.0991	0.1039	-0.0145	-0.0352	0.155	0.0522	0.0166	0.1239	0.0049	-0.0025	0.1206	0.0078	0.1215	0.6212	72.51	10.0538
2	0.7779	-0.6826	0.9018	3.8228	-1.3454	1.666	-0.0963	0.0031	0.0305	0.2294	0.0741	0.0734	-0.1813	-0.0242	0.0405	0.1874	-0.0029	0.0383	0.191	-0.015	0.1528	1.5505	85.8996	-3.5264
3	1.5733	0.8363	0.5896	1.5197	0.1078	1.1001	-0.0075	0.0204	0.0279	-0.0833	0.0405	0.0913	0.0053	-0.0083	-0.0413	0.1547	0.0045	0.0181	0.1285	-0.005	0.1237	-8.8353	74.0678	-10.2414
4	2.754	2.3962	1.2567	6.1937	-1.1401	2.5152	-0.0603	0.0196	0.3185	-0.2371	0.0589	0.436	0.0781	-0.1589	-0.0584	0.1481	-0.0096	-0.0132	0.2057	0.0202	0.1842	-25.812	67.9278	-19.1656
5	1.216	-1.167	-0.7206	1.7853	-0.3243	1.9579	0.0946	-0.0789	0.0387	-0.3901	-0.1394	-0.2384	-0.4513	-0.2178	0.0154	0.7125	0.0952	0.025	0.4854	-0.0071	0.6443	-22.9823	81.0192	-6.894
6	1.7557	0.7489	0.7566	2.8344	-0.4317	2.827	-0.0269	0.1178	-0.0499	-0.1791	0.1052	-0.022	0.0783	-0.0037	-0.1098	0.1177	-0.0118	0.0153	0.1286	-0.0262	0.1329	-5.8674	70.8621	-13.217
7	6.408	4.0569	2.8775	5.4563	1.2918	3.2584	-0.2212	0.3758	0.2708	-0.4703	0.3262	0.4742	-0.1018	-0.0578	-0.0628	0.2205	-0.0111	0.0016	0.2236	0.0413	0.1454	-7.0818	85.6622	-21.9516
8	2.8746	-0.7102	1.3386	2.743	-0.2554	2.5053	-0.0726	0.096	0.1816	-0.105	-0.0218	-0.0571	-0.1403	-0.0329	0.0829	0.1181	-0.0003	0.0017	0.1376	0.0195	0.1122	-3.5496	37.2993	-2.6742
9	0.0838	-0.4334	0.2464	4.1449	-1.9738	2.697	-0.0438	0.0682	0.0353	-0.0965	0.2205	0.323	0.2942	-0.1308	-0.1421	0.1141	-0.0173	-0.0137	0.1573	0.0105	0.1585	3.7216	24.032	8.4456
10	1.1618	-0.6365	-0.694	1.0273	0.615	1.3325	-0.0242	-0.0103	0.0762	0.0994	0.0215	-0.0598	0.0186	0.0073	-0.0022	0.1265	-0.0106	-0.0373	0.1386	-0.0003	0.1644	-1.4548	36.1131	19.5542
11	1.8118	-2.8496	-1.1527	4.7442	2.1886	2.2334	-0.2269	-0.1146	-0.0353	0.8387	0.0497	0.3333	0.2657	-0.151	-0.0021	0.2915	-0.0019	0.0219	0.2183	0.0007	0.2192	-10.93	42.733	35.8728
12	2.5557	0.6125	0.0477	1.8714	-0.4409	1.9277	0.01	0.0086	-0.0913	0.139	0.075	0.2708	0.1069	-0.2896	-0.1897	0.1848	0.0223	-0.0216	0.1724	-0.0083	0.1788	-7.4089	35.7148	17.9117
13	0.6284	0.0111	-0.0237	1.716	0.1191	1.8414	-0.0799	-0.1316	0.0298	0.3474	0.1093	-0.2272	0.0568	0.1306	0.0298	0.16	0.0228	-0.0633	0.1831	0.0014	0.1848	7.1438	32.2118	27.3798
14	4.117	-1.4755	1.331	1.8668	-1.5019	3.6597	-0.1201	-0.3872	-0.0623	0.327	0.0529	-0.094	-0.0235	-0.1184	0.0675	0.2366	-0.0318	-0.0106	0.2242	0.0214	0.1633	-25.2527	37.0642	9.4809
15	3.6392	0.1891	0.3879	7.5401	3.4617	3.1545	-0.1123	0.2743	-0.5919	-0.0964	0.1599	-0.2067	0.7696	-0.0345	-0.0125	0.3056	-0.036	-0.0024	0.2323	0.0106	0.2857	-35.4843	27.3956	-6.4264
16	3.9712	1.284	-1.9313	1.6559	-0.8466	1.6557	-0.0117	0.0326	0.0342	-0.0356	0.0346	0.0849	0.0465	-0.0982	-0.0225	0.1402	-0.013	-0.0415	0.1502	0.0198	0.117	-26.6519	44.3455	-11.0158
17	3.7121	3.5511	0.7769	7.182	0.6735	2.7783	-0.3942	0.5361	0.1237	-0.6608	0.5023	-0.5535	-0.1698	0.3435	-0.0973	0.2609	-0.0305	0.0439	0.2807	0.0204	0.229	-16.0947	54.0853	-24.6009
18	2.1005	-1.5985	-0.0615	2.6955	-0.4016	1.4362	0.0694	0.2281	-0.0477	-0.1539	-0.0087	-0.0568	0.0551	0.1066	-0.1086	0.1142	-0.0329	-0.0358	0.1895	0.0003	0.1304	-20.4013	41.9325	-9.8659
19	0.6717	-0.2373	0.0503	2.9367	0.0754	0.9907	-0.0011	0.3278	0.0388	-0.3271	-0.0203	0.3746	0.1183	-0.1945	0.0284	0.1858	-0.0241	-0.0732	0.3142	0.0169	0.2047	-35.4878	44.9539	-19.407
20	6.1423	-0.6926	0.1749	6.2511	-0.034	4.9832	0.1617	0.2847	0.1999	-0.8103	-0.1073	0.0792	-0.0446	-0.5492	-0.0424	0.2736	0.0625	-0.0096	0.2685	0.0603	0.1448	-21.4799	72.4096	13.6621
21	3.1637	-0.4137	-0.757	0.9346	-1.4345	4.9201	0.1602	0.5353	0.3228	-0.342	-0.0103	-0.0475	-0.707	-0.5867	-0.0953	0.4248	0.098	0.0151	0.3828	0.0792	0.3754	-24.6708	76.08	11.2167
22	3.494	-1.6978	-0.3678	2.225	0.0393	1.9126	0.0396	0.0081	0.185	0.1192	0.0695	0.0952	-0.3338	-0.2733	-0.0765	0.2054	0.0224	0.041	0.1462	0.029	0.1589	-17.5864	70.3294	29.6415
23	1.8351	-0.8954	-0.6288	2.9399	1.8598	3.4442	-0.0565	-0.3284	0.0409	0.4902	0.1926	-1.0748	0.3086	0.4169	-0.1421	0.2112	0.0203	-0.0536	0.2642	0.016	0.3116	0.6944	56.5928	35.7412
24	1.8953	0.798	2.2203	7.0445	-4.5409	7.3752	0.0767	0.0492	-0.0337	0.7724	-0.2909	-0.2336	-0.725	0.5762	0.3348	0.29	-0.0462	0.0141	0.36	-0.0997	0.2693	0.7793	73.4726	28.4866
25	1.0125	0.1674	-0.2745	2.0004	-0.6986	2.2653	0.0335	0.0482	0.056	0.0843	0.0659	0.1741	0.0389	-0.1938	-0.1015	0.1093	0.0046	0.0308	0.1462	0.0044	0.1409	-17.6777	63.3357	31.1724
26	8.4542	-6.304	1.9588	8.8686	-1.9387	3.7156	0.4471	-0.3177	0.2501	0.4375	-0.2986	-0.0901	-0.2921	0.0013	-0.1139	0.4892	-0.0765	0.0305	0.2435	-0.052	0.2081	-15.1679	72.5304	44.9424

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 52 THROUGH 118 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 119 THROUGH 159 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 160 THROUGH 226 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 227 THROUGH 258 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 259 THROUGH 277 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 278 THROUGH 341 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 342 THROUGH 364 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 50 THROUGH 118 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 119 THROUGH 159 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 160 THROUGH 226 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 227 THROUGH 258 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 259 THROUGH 308 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 309 THROUGH 364 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 52 THROUGH 126 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 127 THROUGH 159 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 160 THROUGH 226 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 227 THROUGH 258 )
18	X-RAY DIFFRACTION	18	CHAIN 'C' AND (RESID 259 THROUGH 308 )
19	X-RAY DIFFRACTION	19	CHAIN 'C' AND (RESID 309 THROUGH 364 )
20	X-RAY DIFFRACTION	20	CHAIN 'D' AND (RESID 52 THROUGH 86 )
21	X-RAY DIFFRACTION	21	CHAIN 'D' AND (RESID 87 THROUGH 137 )
22	X-RAY DIFFRACTION	22	CHAIN 'D' AND (RESID 138 THROUGH 226 )
23	X-RAY DIFFRACTION	23	CHAIN 'D' AND (RESID 227 THROUGH 258 )
24	X-RAY DIFFRACTION	24	CHAIN 'D' AND (RESID 259 THROUGH 277 )
25	X-RAY DIFFRACTION	25	CHAIN 'D' AND (RESID 278 THROUGH 341 )
26	X-RAY DIFFRACTION	26	CHAIN 'D' AND (RESID 342 THROUGH 364 )

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