PDB-3dl2: Hexagonal structure of the LDH domain of Human Ubiquitin-conjugat...

ID or keywords:

Entry

Database: PDB / ID: 3dl2

Title

Hexagonal structure of the LDH domain of Human Ubiquitin-conjugating Enzyme E2-like Isoform A

Components

Ubiquitin-conjugating enzyme E2 variant 3

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / L-LACTATE DEHYDROGENASE / OXIDOREDUCTASE / UBIQUITIN-PROTEIN LIGASE / Alternative splicing / NAD / Ubl conjugation pathway / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

ESCRT I complex / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / endosome to lysosome transport / ubiquitin binding / protein modification process / protein transport / extracellular exosome
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Finerty Jr., P.J. / Butler-Cole, C. / Bountra, C. / Wolkstrom, M. / Arrowsmith, C.H. / Edwards, A.M. ...

Citation

Journal: To be Published
Title: Structural Investigation Into the L-Lactate Dehydrogenase Domain of Human Ubiquitin-Conjugating Enzyme E2-Like Isoform A.
Authors: Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Finerty Jr., P.J. / Butler-Cole, C. / Bountra, C. / Wolkstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.

History

Deposition	Jun 26, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 15, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3dl2.cif.gz	236.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3dl2.ent.gz	192.3 KB	Display	PDB format
PDBx/mmJSON format	3dl2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3dl2_validation.pdf.gz	446.9 KB	Display	wwPDB validaton report
Full document	3dl2_full_validation.pdf.gz	449.7 KB	Display
Data in XML	3dl2_validation.xml.gz	23.1 KB	Display
Data in CIF	3dl2_validation.cif.gz	32.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dl/3dl2 ftp://data.pdbj.org/pub/pdb/validation_reports/dl/3dl2	HTTPS FTP

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Related structure data

Related structure data	1i10S 2i6t S: Starting model for refinement
Similar structure data	2i6t-d 3sie-d 5nkk-1 6vdj-d 6p3h-2 4v0g-d 4uum-d 4rwg-1 5y40-d 3ps5-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 (6) #154 - Oct 2012 Citric Acid Cycle similarity (6) #234 - Jun 2019 MDM2 and Cancer similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #142 - Oct 2011 PDB Pioneers similarity (6)

Deposited unit

A: Ubiquitin-conjugating enzyme E2 variant 3

B: Ubiquitin-conjugating enzyme E2 variant 3

hetero molecules

66 kDa, 2 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)	105.603, 105.603, 131.918
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Ubiquitin-conjugating enzyme E2 variant 3 / UEV-3 / EV and lactate/malate dehydrogenase domain-containing protein Mass: 32821.367 Da / Num. of mol.: 2 / Fragment: L-lactate dehydrogenase domain, residues 171-471 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UEVLD, UEV3 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IX04
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.23 Å³/Da / Density % sol: 61.98 %
Crystal grow	Temperature: 290.9 K / pH: 6.5 Details: 1.6 M Sodium/potassium phosphate pH 6.5, 0.2 M Sodium chloride, 0.002 M Dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 11, 2006
Radiation	Monochromator: SI(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.1→28 Å / Num. obs: 47978 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / R_sym value: 0.08 / Net I/σ(I): 28.929
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 9 % / Mean I/σ(I) obs: 3.32 / R_sym value: 0.735 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I10

1i10

Resolution: 2.1→27.97 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.947 / SU B: 8.214 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2255	2402	5 %	RANDOM
R_work	0.19463	-	-	-
obs	0.1962	45317	98.88 %	-
all	-	47978	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 27.702 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.48 Å²	0.74 Å²	0 Å²
2-	-	1.48 Å²	0 Å²
3-	-	-	-2.22 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→27.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4354	0	17	203	4574

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	4424
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.006	1.958	6007
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.914	5	575
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.869	25.506	158
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.147	15	775
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.368	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	744
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3153
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.184	0.2	1968
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.287	0.2	3104
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.109	0.2	252
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.192	0.2	72
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.135	0.2	20
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.348	1.5	2871
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.68	2	4642
X-RAY DIFFRACTION	r_scbond_it	1.143	3	1610
X-RAY DIFFRACTION	r_scangle_it	1.892	4.5	1365
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.16 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.294	175	-
R_work	0.24	3045	-
obs	-	-	90.96 %

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	3.4571	1.1138	-0.8794	1.1525	0.8475	5.0125	0.2926	-0.9453	0.1367	0.1107	-0.2291	0.1649	-0.4282	0.188	-0.0634	0.2136	-0.0635	-0.0107	0.3675	0.0118	0.2055	-25.1932	37.9141	27.8306
2	8.4938	-1.6968	-1.2417	36.8415	2.3062	11.0338	0.0889	-0.3947	0.0295	0.1087	-0.3135	0.0475	-0.5174	-0.7781	0.2246	0.1022	0.0219	-0.0411	0.2451	0.0015	0.1217	-31.5292	35.1801	19.7552
3	8.879	-2.0908	-2.7341	1.1005	-1.8426	15.1711	-0.1595	0.3115	-0.394	-0.7169	0.0327	0.5087	0.1435	-0.6793	0.1268	0.2126	-0.0663	0.0054	0.1835	-0.0206	0.1716	-32.3857	29.8298	28.2918
4	6.6048	1.2488	0.7645	0.494	1.1025	3.6469	0.1536	-0.2398	-0.7768	0.0036	-0.0847	-0.0819	0.3092	-0.0513	-0.0689	0.2047	0.0275	-0.0706	0.1093	0.0461	0.2627	-26.4388	28.4731	13.8873
5	3.7804	0.5103	0.6785	2.8356	1.4315	2.447	0.0839	0.1301	-0.2843	-0.0804	0.0415	-0.2038	-0.0072	0.2041	-0.1254	0.1895	0.0317	-0.042	0.1013	0.011	0.1742	-21.8816	28.8366	6.5284
6	6.8131	2.3644	4.8352	1.2102	1.8622	3.5186	-0.1061	-0.1221	0.1901	-0.2176	-0.0176	0.0142	-0.3676	-0.1664	0.1237	0.1961	-0.0448	0.0069	0.194	0.0581	0.222	-6.966	42.4299	17.6992
7	6.0202	3.8097	13.4058	2.4108	8.4872	30.2602	-1.5264	0.2634	1.2379	-1.5585	0.5059	0.1186	-3.6796	0.3319	1.0206	0.4271	-0.1212	-0.0468	0.2918	0.0886	0.3929	-0.0744	48.6942	14.4344
8	12.4142	11.2925	0.6261	15.6704	-1.7424	3.9915	0.1982	0.0592	0.3621	0.131	-0.2838	-0.2981	-0.5946	0.745	0.0856	0.1528	-0.0669	0.0572	0.3285	-0.0221	0.1595	0.8684	42.0105	11.2547
9	11.7196	11.0474	-5.8321	13.6488	-6.4051	4.6365	-0.0159	0.4911	-0.1107	-0.1127	0.2112	0.0108	0.0308	-0.2255	-0.1953	0.1619	-0.0189	-0.0228	0.1558	0.0311	0.2177	7.3851	42.0239	17.728
10	3.5252	0.4245	0.0971	1.895	0.2482	4.488	-0.0143	0.3435	0.1367	-0.3033	-0.0287	-0.0867	-0.4638	0.1814	0.043	0.2223	-0.0438	-0.0213	0.1506	0.0586	0.1917	-13.4436	41.22	9.8533
11	7.4501	-1.0026	0.6028	5.9845	1.7083	4.4127	-0.1583	0.8486	-0.1665	-0.3032	0.4382	-0.8282	-0.1902	0.9707	-0.2799	0.104	-0.0295	0.0689	0.352	-0.0325	0.0313	-5.5796	33.2228	1.8611
12	1.917	1.2155	0.1288	2.4831	-1.6258	4.7987	-0.3854	0.4429	0.225	-0.5001	0.4053	0.0013	-0.1543	-0.3379	-0.0198	0.2479	-0.074	0.0034	0.2516	-0.0226	0.2031	-19.0315	41.6376	33.4471
13	0.4084	1.2563	-1.6982	4.5153	-2.8554	15.673	-0.2716	-0.5361	0.218	0.4064	0.0549	-0.3822	-0.6373	0.4154	0.2167	0.1823	-0.0265	-0.0115	0.2656	-0.0041	0.2181	-9.8028	43.156	32.2181
14	2.7528	4.064	0.7945	6.2518	0.1866	4.0896	-0.1282	0.0642	-0.395	-0.0006	0.1262	-0.818	0.174	0.2252	0.002	0.1552	0.0662	-0.0142	0.1642	-0.0676	0.2714	-11.9876	36.9418	46.3895
15	3.2017	1.0004	1.3272	2.6308	0.4328	2.4711	0.0707	-0.0125	-0.3667	0.1246	0.0988	-0.199	0.1609	-0.01	-0.1695	0.1557	0.0506	-0.0135	0.1554	-0.0461	0.2018	-13.5944	33.0609	52.8815
16	4.8114	3.225	3.9092	3.2883	3.2405	3.5998	-0.1856	-0.269	-0.0551	-0.0375	0.1094	0.0352	-0.2387	-0.2979	0.0762	0.1572	0.0092	0.0511	0.2139	-0.0195	0.1815	-29.8553	29.246	45.9156
17	6.9765	5.9128	5.6994	5.3807	3.1856	11.9777	0.1	-0.583	-0.0823	0.2063	-0.1067	0.1792	0.2697	-1.0137	0.0067	0.2302	-0.1127	0.0825	0.2315	-0.0154	0.1588	-34.9803	20.8949	46.4827
18	21.4225	0.1223	-10.7985	2.6718	0.98	11.4718	0.5822	-0.5443	0.6853	0.2008	-0.0955	0.1717	-0.486	-0.101	-0.4868	0.1013	-0.0127	0.0424	0.1525	-0.0116	0.1883	-45.2545	15.924	45.8191
19	15.5219	18.2831	-1.3207	25.7747	0.1924	0.8332	-0.0819	0.5677	-1.2076	0.1097	0.2033	-1.5249	-0.3366	0.0826	-0.1214	0.1121	-0.0311	0.0007	0.2385	-0.0491	0.2985	-27.0665	19.6088	36.1251
20	2.5405	0.8583	0.4578	2.3779	0.4495	4.1121	0.0173	-0.344	0.0303	0.2762	-0.0275	0.1827	-0.0714	-0.5017	0.0103	0.116	0.0163	0.0384	0.227	-0.0486	0.173	-29.0318	32.4044	50.3045
21	5.1655	-2.1544	2.6221	18.0246	-0.5107	2.6497	0.398	-0.9059	-0.6798	0.4885	-0.1144	2.3835	0.7457	-1.3877	-0.2836	0.2322	-0.2589	0.1342	0.4702	0.051	0.2427	-35.9706	21.392	56.9718
22	32.3122	14.4784	1.2907	7.8717	-2.6208	7.4451	0.8954	-0.6715	-1.0575	0.9823	-0.6611	-0.8608	0.8904	0.6314	-0.2343	0.2355	0.0062	-0.1359	0.0406	0.0927	0.2128	-15.469	19.722	59.8284

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	169 - 206	1 - 38
2	X-RAY DIFFRACTION	2	A	A	207 - 215	39 - 47
3	X-RAY DIFFRACTION	3	A	A	216 - 235	48 - 67
4	X-RAY DIFFRACTION	4	A	A	236 - 263	68 - 95
5	X-RAY DIFFRACTION	5	A	A	264 - 310	96 - 142
6	X-RAY DIFFRACTION	6	A	A	311 - 335	143 - 167
7	X-RAY DIFFRACTION	7	A	A	336 - 346	168 - 178
8	X-RAY DIFFRACTION	8	A	A	347 - 362	179 - 194
9	X-RAY DIFFRACTION	9	A	A	363 - 385	195 - 217
10	X-RAY DIFFRACTION	10	A	A	386 - 436	218 - 268
11	X-RAY DIFFRACTION	11	A	A	437 - 471	269 - 303
12	X-RAY DIFFRACTION	12	B	B	169 - 214	1 - 46
13	X-RAY DIFFRACTION	13	B	B	215 - 235	47 - 67
14	X-RAY DIFFRACTION	14	B	B	236 - 263	68 - 95
15	X-RAY DIFFRACTION	15	B	B	264 - 304	96 - 136
16	X-RAY DIFFRACTION	16	B	B	305 - 335	137 - 167
17	X-RAY DIFFRACTION	17	B	B	336 - 356	168 - 188
18	X-RAY DIFFRACTION	18	B	B	357 - 378	189 - 210
19	X-RAY DIFFRACTION	19	B	B	379 - 387	211 - 219
20	X-RAY DIFFRACTION	20	B	B	388 - 437	220 - 269
21	X-RAY DIFFRACTION	21	B	B	438 - 456	270 - 288
22	X-RAY DIFFRACTION	22	B	B	457 - 471	289 - 303

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