PDB-2eso: Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala

ID or keywords:

Entry

Database: PDB / ID: 2eso

Title

Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala

Components

Ubiquitin-conjugating enzyme E2 D2

Keywords

LIGASE

Function / homology

Function and homology information

(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein autoubiquitination / protein K48-linked ubiquitination / ubiquitin ligase complex / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / Negative regulators of DDX58/IFIH1 signaling ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Ozkan, E. / Yu, H. / Deisenhofer, J.

Citation

Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Mechanistic insight into the allosteric activation of a ubiquitin-conjugating enzyme by RING-type ubiquitin ligases
Authors: Ozkan, E. / Yu, H. / Deisenhofer, J.

History

Deposition	Oct 26, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 6, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.4	Oct 20, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5	Aug 23, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2eso.cif.gz	51 KB	Display	PDBx/mmCIF format
PDB format	pdb2eso.ent.gz	36.2 KB	Display	PDB format
PDBx/mmJSON format	2eso.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2eso_validation.pdf.gz	423.2 KB	Display	wwPDB validaton report
Full document	2eso_full_validation.pdf.gz	425.4 KB	Display
Data in XML	2eso_validation.xml.gz	10.1 KB	Display
Data in CIF	2eso_validation.cif.gz	14.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/es/2eso ftp://data.pdbj.org/pub/pdb/validation_reports/es/2eso	HTTPS FTP

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Related structure data

Related structure data	2eskSC 2espC 2esqC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2c4p-2 1jzw-d 2esq-d 2c4p-1 2r0j-d 2esk-d 5egg-d 1s3d-d 1z3d-d 6cyo-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	#234 - Jun 2019 MDM2 and Cancer similarity (13) #60 - Dec 2004 Ubiquitin similarity (11) #143 - Nov 2011 Toll-like Receptors similarity (1) #56 - Aug 2004 Caspases similarity (1)

Deposited unit

A: Ubiquitin-conjugating enzyme E2 D2

16.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	47.654, 49.429, 63.037
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin-protein ligase D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2-17 kDa ...Ubiquitin-protein ligase D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / E217 / KB 2 Mass: 16841.277 Da / Num. of mol.: 1 / Mutation: I37A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, UBC4, UBCH5B / Plasmid: pHis-parallel / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62837, ubiquitin-protein ligase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Ubiquitin-conjugating enzyme E2 D2 / Ubiquitin-protein ligase D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2-17 kDa ...

Mass: 16841.277 Da / Num. of mol.: 1 / Mutation: I37A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: UBE2D2, UBC4, UBCH5B / Plasmid: pHis-parallel / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62837, ubiquitin-protein ligase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.2 Å³/Da / Density % sol: 44 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: NaCl, PEG 6000, Sodium Acetate, temperature 294K, pH 4.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97897 Å
Detector	Type: SBC-3 / Detector: CCD / Date: Jul 15, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97897 Å / Relative weight: 1
Reflection	Resolution: 1.5→50 Å / Num. obs: 24280 / % possible obs: 99 % / Redundancy: 9.4 % / R_merge(I) obs: 0.058 / Net I/σ(I): 42.6
Reflection shell	Resolution: 1.5→1.55 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.796 / Mean I/σ(I) obs: 2.6

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Phasing

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.5 Å	38.9 Å
Translation	2.5 Å	38.9 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1.7	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ESK

2esk

Resolution: 1.5→38.9 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.949 / SU B: 2.686 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21913	1231	5.1 %	RANDOM
R_work	0.17723	-	-	-
obs	0.17938	23013	98.89 %	-

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: 22.78 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.34 Å²	0 Å²	0 Å²
2-	-	-0.32 Å²	0 Å²
3-	-	-	-0.02 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→38.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1184	0	0	178	1362

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	1258
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.067	1.965	1728
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	18.176	5	161
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.205	23.636	55
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.664	15	204
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.524	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.169	0.2	188
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	984
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	612
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.325	0.2	876
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	123
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	0.191	0.2	50
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.205	0.2	28
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	1.298	1.5	797
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.634	2	1277
X-RAY DIFFRACTION	r_scbond_it	2.762	3	529
X-RAY DIFFRACTION	r_scangle_it	4.066	4.5	445
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.499-1.538	0.307	84	0.289	1635	1779	96.627
1.538-1.58	0.261	103	0.261	1633	1736	100
1.58-1.626	0.291	67	0.222	1597	1665	99.94
1.626-1.676	0.229	64	0.205	1585	1649	100
1.676-1.731	0.24	87	0.189	1516	1605	99.875
1.731-1.791	0.211	74	0.193	1462	1537	99.935
1.791-1.859	0.281	74	0.185	1429	1508	99.668
1.859-1.935	0.192	66	0.174	1352	1422	99.719
1.935-2.02	0.173	58	0.166	1326	1388	99.712
2.02-2.119	0.214	70	0.165	1250	1330	99.248
2.119-2.233	0.221	62	0.161	1195	1262	99.604
2.233-2.368	0.207	65	0.173	1131	1208	99.007
2.368-2.531	0.189	60	0.18	1050	1122	98.93
2.531-2.733	0.21	64	0.184	986	1063	98.777
2.733-2.992	0.218	65	0.183	905	987	98.278
2.992-3.343	0.185	54	0.169	816	893	97.424
3.343-3.855	0.226	34	0.157	731	792	96.591
3.855-4.71	0.224	32	0.145	629	684	96.637
4.71-6.612	0.186	24	0.2	498	545	95.78
6.612-38.895	0.322	24	0.185	287	340	91.471

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	7.3939	-0.8534	2.9347	5.3506	-0.6595	1.8625	0.3478	0.2203	0.2693	-0.5056	-0.3513	-0.7003	0.332	0.1523	0.0035	0.0048	0.0446	0.0822	-0.008	0.0288	0.0665	34.539	-6.087	57.767
2	25.685	7.6439	-2.1568	9.4445	-1.4277	6.0557	-0.412	0.3103	0.0306	-0.6326	0.3152	0.2348	0.4763	-0.1223	0.0968	0.1195	-0.0035	-0.0329	-0.0237	0.0107	-0.0028	22	-6.587	51.661
3	15.06	4.4162	-0.9501	7.5986	-0.4238	1.7303	-0.3882	0.3475	0.235	-0.4319	0.3228	-0.1986	0.0176	-0.0296	0.0654	-0.0389	-0.0055	0.0211	-0.0445	0.0013	-0.0579	24.733	3.35	57.146
4	5.6798	0.1532	2.7381	2.3177	-2.3617	3.884	0.0425	0.127	0.2536	-0.0645	-0.0648	-0.4053	0.1788	0.2236	0.0223	-0.0546	0.0124	0.024	-0.0443	-0.0044	0.0438	30.715	2.108	61.182
5	23.333	8.2372	4.5538	6.9108	3.074	1.4259	-0.3044	0.743	0.2812	-0.4081	0.1993	0.1372	-0.0946	-0.0336	0.1051	-0.0563	-0.0301	-0.0142	-0.0048	0.0067	-0.0431	16.687	2.712	59.532
6	6.4904	3.8447	1.3333	13.0719	1.3817	4.8287	-0.0316	0.1661	-0.1527	-0.2228	-0.097	0.2657	0.2189	-0.3603	0.1286	-0.0435	-0.0073	-0.0365	-0.0345	-0.0093	-0.0188	3.239	-3.25	62.038
7	8.1569	2.1807	-1.258	2.3473	-0.3391	1.285	-0.1018	0.263	0.4046	-0.1504	0.1216	0.1698	0.0229	-0.015	-0.0198	-0.075	0.0053	-0.0284	-0.0748	0.0021	-0.0305	11.344	3.367	63.289
8	4.1794	-3.5979	-0.7954	8.0303	1.2718	2.5184	-0.0762	-0.19	0.3522	0.295	0.1664	-0.5807	0.0336	0.1665	-0.0902	-0.0838	0.0168	-0.0305	-0.0168	-0.0166	0.013	32.565	-4.861	66.269
9	18.9712	-22.226	-2.2321	26.9023	1.9956	2.4767	-0.5741	-0.5417	0.4714	0.7758	0.6769	-0.6814	0.1626	0.1155	-0.1029	-0.0535	0.0257	-0.0348	-0.0088	-0.022	-0.0238	27.399	-3.616	70.066
10	13.3103	-1.0208	-1.6485	3.2735	-2.8484	2.9739	-0.0537	-0.4939	0.6605	0.1569	0.1098	0.0068	-0.1837	-0.0146	-0.0561	-0.0429	0.023	-0.0286	-0.0535	-0.0517	0.0033	13.534	6.019	69.571
11	7.6622	0.0945	-1.2617	0.6731	-0.9296	4.8211	-0.0065	-0.3152	0.1474	0.1356	-0.0121	0.0674	0.006	0.0302	0.0186	-0.0258	0.0209	0.01	-0.0205	-0.033	-0.0702	10.776	0.368	75.283
12	6.7994	-6.5039	-3.1015	15.5904	3.7852	3.4195	-0.2161	-0.3185	-0.2102	0.3095	0.1025	-0.0474	0.2881	0.1001	0.1137	-0.0157	0.0289	-0.003	0.0312	0.0111	-0.0791	19.473	-4.373	73.367
13	8.69	-3.5124	-3.5405	5.0693	1.8662	10.9184	-0.3211	-0.5848	-0.1173	0.7689	0.337	-0.0629	0.2866	0.1952	-0.0159	0.0549	0.0437	0.0006	-0.0255	0.0187	-0.0246	26.247	-12.791	70.103
14	10.9971	-0.0855	-1.8314	1.9455	-0.5531	2.207	-0.115	-0.0462	-0.0048	0.0593	-0.0062	0.0125	0.0712	0.0365	0.1212	-0.0481	-0.0051	0.0067	-0.0961	-0.013	-0.0576	17.456	-7.581	63.75
15	4.9593	1.2979	9.1734	8.5773	1.7181	50.4575	-0.0601	-0.1794	0.1042	1.2553	-0.4206	0.1234	1.3356	0.3986	0.4807	0.1886	-0.0073	0.0445	-0.0163	-0.0295	0.043	9.573	-8.95	76.007
16	2.0486	-1.3457	-3.7365	0.9608	2.8033	8.3989	0.018	0.0757	-0.1847	0.0772	-0.2052	0.1574	0.4365	0.0639	0.1872	0.0514	-0.0467	0.0276	0.0163	-0.018	-0.0484	5.607	-2.674	80.705
17	2.9275	2.8501	0.9803	18.4615	-7.7384	21.6725	0.1167	0.1578	-0.0951	0.6172	-0.1005	0.902	0.2217	-0.4918	-0.0162	-0.0058	-0.0772	0.1066	0.0685	-0.0872	0.0587	-2.517	-4.944	77.348
18	10.0438	5.2429	-0.6653	17.5737	-10.6303	9.9246	-0.2412	-0.3381	0.1927	0.1009	0.1357	0.3934	0.1683	-0.6319	0.1055	-0.0362	0.0101	0.0367	0.0381	-0.0871	0.0364	-0.595	0.833	72.707
19	9.4644	2.4179	2.9953	13.104	3.6026	18.9124	0.0957	-0.4304	0.7874	0.4694	-0.0826	0.7448	0.2512	-0.5128	-0.013	-0.0628	0.0355	-0.0117	-0.0656	-0.0543	0.0953	1.941	5.826	69.803
20	6.6794	3.5925	3.301	9.9943	4.5565	7.0728	0.0559	-0.0893	0.5869	-0.0314	-0.043	0.0834	-0.2483	-0.2577	-0.0129	-0.0533	0.0409	-0.0338	-0.0755	0.0099	0.1066	5.386	10.245	66.181

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	-1 - 10	1 - 12
2	X-RAY DIFFRACTION	2	A	A	11 - 19	13 - 21
3	X-RAY DIFFRACTION	3	A	A	20 - 29	22 - 31
4	X-RAY DIFFRACTION	4	A	A	30 - 33	32 - 35
5	X-RAY DIFFRACTION	5	A	A	34 - 38	36 - 40
6	X-RAY DIFFRACTION	6	A	A	39 - 44	41 - 46
7	X-RAY DIFFRACTION	7	A	A	45 - 53	47 - 55
8	X-RAY DIFFRACTION	8	A	A	54 - 62	56 - 64
9	X-RAY DIFFRACTION	9	A	A	63 - 68	65 - 70
10	X-RAY DIFFRACTION	10	A	A	69 - 73	71 - 75
11	X-RAY DIFFRACTION	11	A	A	74 - 80	76 - 82
12	X-RAY DIFFRACTION	12	A	A	81 - 89	83 - 91
13	X-RAY DIFFRACTION	13	A	A	90 - 97	92 - 99
14	X-RAY DIFFRACTION	14	A	A	98 - 110	100 - 112
15	X-RAY DIFFRACTION	15	A	A	111 - 118	113 - 120
16	X-RAY DIFFRACTION	16	A	A	119 - 127	121 - 129
17	X-RAY DIFFRACTION	17	A	A	128 - 133	130 - 135
18	X-RAY DIFFRACTION	18	A	A	134 - 138	136 - 140
19	X-RAY DIFFRACTION	19	A	A	139 - 142	141 - 144
20	X-RAY DIFFRACTION	20	A	A	143 - 147	145 - 149

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