PDB-2esp: Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala

ID or keywords:

Entry

Database: PDB / ID: 2esp

Title

Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala

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 K48-linked ubiquitination / protein autoubiquitination / 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: 1.52 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 / Derived calculations / Category: database_2 / 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
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	2esp.cif.gz	50.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2esp.ent.gz	35.6 KB	Display	PDB format
PDBx/mmJSON format	2esp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/es/2esp ftp://data.pdbj.org/pub/pdb/validation_reports/es/2esp	HTTPS FTP

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Related structure data

Related structure data	2eskSC 2esoC 2esqC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2esk-d 2c4p-2 1s3d-d 1jzw-d 5egg-d 1j9b-d 2eso-d 1sd8-d 1sk0-d 2esq-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

hetero molecules

17 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)	47.877, 49.224, 62.128
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: I88A 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: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 136 / 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: 43 %
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: 1.52→50 Å / Num. obs: 22996 / % possible obs: 98.7 % / Redundancy: 4.9 % / R_merge(I) obs: 0.045 / Net I/σ(I): 31.6
Reflection shell	Resolution: 1.52→1.57 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.522 / Mean I/σ(I) obs: 2.2 / % possible all: 91

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Phasing

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.5 Å	34.32 Å
Translation	2.5 Å	34.32 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: 1.52→38.58 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.946 / SU B: 2.95 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23342	1168	5.1 %	RANDOM
R_work	0.18415	-	-	-
obs	0.18663	21765	98.76 %	-

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: 18.722 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.18 Å²	0 Å²	0 Å²
2-	-	-0.35 Å²	0 Å²
3-	-	-	0.53 Å²

Refinement step

Cycle: LAST / Resolution: 1.52→38.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1184	0	9	136	1329

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	1261
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.084	1.968	1731
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	13.488	5	160
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.036	23.455	55
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.101	15	201
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.492	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.138	0.2	188
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	982
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	606
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.326	0.2	887
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	102
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	0.169	0.2	52
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.139	0.2	15
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	1.182	1.5	795
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.595	2	1270
X-RAY DIFFRACTION	r_scbond_it	2.662	3	533
X-RAY DIFFRACTION	r_scangle_it	4.035	4.5	456
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 (%)
1.52-1.559	0.318	86	0.272	1405	1668	89.388
1.559-1.602	0.302	80	0.244	1521	1654	96.796
1.602-1.648	0.302	59	0.232	1525	1597	99.186
1.648-1.699	0.298	78	0.223	1463	1546	99.677
1.699-1.755	0.25	76	0.218	1442	1518	100
1.755-1.816	0.248	73	0.206	1391	1464	100
1.816-1.885	0.257	60	0.185	1364	1425	99.93
1.885-1.961	0.217	62	0.184	1288	1352	99.852
1.961-2.048	0.255	61	0.169	1249	1316	99.544
2.048-2.148	0.204	74	0.168	1192	1266	100
2.148-2.264	0.211	62	0.166	1124	1188	99.832
2.264-2.401	0.236	55	0.181	1069	1130	99.469
2.401-2.566	0.206	63	0.177	1012	1075	100
2.566-2.77	0.2	58	0.187	939	997	100
2.77-3.033	0.218	59	0.199	870	932	99.678
3.033-3.388	0.28	51	0.172	789	845	99.408
3.388-3.908	0.194	32	0.151	724	759	99.605
3.908-4.774	0.225	33	0.17	616	649	100
4.774-6.7	0.289	24	0.198	493	518	99.807
6.7-38.576	0.22	22	0.193	289	322	96.584

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	14.1283	4.9742	2.1334	4.6031	1.6853	4.3376	0.0863	0.0567	0.0605	-0.0117	0.0214	-0.3217	0.0646	0.231	-0.1078	-0.0492	0.0226	0.0017	-0.0149	-0.0057	0.0018	37.754	-6.897	58.813
2	6.8662	0.6788	1.4521	6.8554	-1.4315	1.722	0.1323	0.027	0.1769	-0.1835	-0.0441	-0.0416	0.0824	0.0461	-0.0882	-0.0394	0.0065	0.0067	-0.0337	-0.0094	-0.0333	31.441	-4.927	54.973
3	15.3181	-4.8643	4.9613	14.0194	-0.0018	5.7878	0.1331	0.5333	-0.5185	-0.355	-0.1915	0.6991	0.0105	0.2098	0.0584	0.0204	0.0149	-0.0356	0.0027	-0.0331	0.0299	24.296	-6.95	49.567
4	43.3612	9.6947	-9.113	16.4181	2.3942	6.9745	-0.9403	1.4006	-0.5279	-0.4713	0.3195	0.5786	0.3558	-0.6293	0.6208	0.0104	-0.0615	-0.0106	0.1122	-0.0326	-0.0665	16.116	-2.819	54.642
5	5.7157	5.8708	1.1299	11.0855	-2.5545	7.7389	-0.1646	0.4569	0.3079	-0.0364	0.195	-0.4122	-0.4368	0.012	-0.0304	0.0006	0.0062	0.0252	-0.0276	-0.0095	0.0409	30.634	6.445	57.203
6	12.6755	-2.729	2.1104	2.9524	-0.9649	2.2285	-0.0236	-0.1541	0.2214	0.1017	0.0619	-0.3725	0.0964	0.0534	-0.0383	-0.0499	-0.0024	-0.0011	-0.0311	-0.0148	-0.0176	30.953	2.201	60.591
7	33.0002	12.3706	0.7986	5.8973	0.9506	0.8715	-0.3391	0.7153	0.0539	-0.1826	0.317	0.0572	0.0039	0.0887	0.0221	-0.0403	-0.0045	-0.0233	-0.0171	0.0124	-0.0385	10.536	-0.671	59.193
8	4.9409	0.9879	0.7303	5.4115	-0.7365	1.1891	0.0523	0.2964	0.2514	-0.0582	0.0665	0.1987	-0.0061	0.1245	-0.1188	-0.0476	0.0124	-0.0098	-0.0187	-0.0026	-0.0446	8.186	2.754	61.921
9	3.3101	-2.0873	-1.0303	3.3682	0.7605	0.3267	-0.0144	-0.0041	0.089	0.0674	0.0309	-0.1372	0.0385	0.0209	-0.0164	-0.0427	0.0005	-0.0242	-0.0033	-0.0095	-0.0271	30.479	-2.28	65.352
10	33.8551	-30.5967	1.6386	30.6176	-0.6381	1.5964	-0.2872	-0.0406	0.2218	0.5437	0.203	-0.1709	0.1129	0.0052	0.0842	-0.0179	0.0155	0.0017	0.0077	0.0101	-0.0587	29.204	-5.266	68.881
11	14.9531	-1.3578	-4.5641	3.7635	-3.5476	5.7055	-0.2206	-0.4491	0.6259	0.1187	0.2949	-0.2016	-0.1738	0.2765	-0.0743	0.0446	0.0183	-0.0565	0.047	-0.0911	0.0679	13.367	5.753	68.589
12	2.2306	-0.3699	-1.965	4.9405	0.0738	4.859	0.0164	-0.0984	-0.1136	0.0723	0.0089	-0.013	-0.1526	0.0402	-0.0253	-0.006	0.0154	0.0076	-0.0075	-0.0066	-0.0744	9.958	-0.585	73.871
13	9.9836	-10.6437	-5.4128	22.5794	4.7782	4.9421	-0.3036	-0.134	-0.0679	0.2819	0.0028	-0.2294	0.0975	0.0666	0.3007	0.0134	-0.0027	-0.0345	0.0824	-0.0007	-0.04	18.884	-3.161	73.175
14	8.8716	-4.306	-1.2415	13.695	5.7102	15.0843	-0.1986	-0.7768	-0.1879	1.11	0.1563	0.2574	0.1543	-0.1595	0.0423	0.0584	0.0015	0.0358	0.0347	0.0131	-0.0246	26.285	-12.657	69.364
15	10.8357	-0.3038	-2.9381	0.86	0.335	1.763	-0.0658	0.0254	0.0103	0.0671	0.0418	-0.0492	0.01	-0.0706	0.024	-0.038	-0.0009	-0.0007	-0.0517	-0.0064	-0.0556	17.41	-7.696	62.898
16	5.6318	3.5289	0.8176	10.3778	-1.5912	30.5808	0.3062	-0.4671	-0.0399	1.2751	-0.5682	0.1388	0.6709	0.911	0.262	0.1557	-0.0296	0.043	0.0504	-0.0191	0.012	9.782	-9.55	74.903
17	4.6801	1.8117	1.3613	2.9156	1.5354	4.4848	-0.0078	-0.0978	-0.1755	0.269	-0.1057	0.0712	0.2984	0.0273	0.1134	0.0235	-0.0026	0.0487	-0.0038	-0.0206	-0.0413	2.878	-3.803	78.529
18	9.5535	-3.2654	3.263	6.0041	-5.1756	11.4446	0.0248	-0.144	0.1292	0.1548	-0.0031	0.3352	-0.1544	-0.4114	-0.0217	0.0115	0.0054	0.0578	-0.0178	-0.0517	0.0472	-2.847	-0.501	71.869
19	2.5607	-0.4559	-0.0148	12.9611	3.9747	13.7799	0.0615	-0.1673	-0.0171	0.6173	-0.186	0.4587	-0.0909	-0.4773	0.1245	-0.0345	0.0243	0.0261	-0.02	-0.0137	0.0279	0.999	5.109	69.601
20	2.4544	2.1422	-1.383	9.9936	2.0789	5.4866	0.0605	0.0516	0.2111	-0.003	0.0342	0.2439	-0.1385	-0.233	-0.0947	-0.0236	0.0233	-0.016	-0.0249	0.0119	0.0165	5.218	9.528	64.729

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 - 5	1 - 7
2	X-RAY DIFFRACTION	2	A	A	6 - 10	8 - 12
3	X-RAY DIFFRACTION	3	A	A	11 - 17	13 - 19
4	X-RAY DIFFRACTION	4	A	A	18 - 23	20 - 25
5	X-RAY DIFFRACTION	5	A	A	24 - 29	26 - 31
6	X-RAY DIFFRACTION	6	A	A	30 - 33	32 - 35
7	X-RAY DIFFRACTION	7	A	A	34 - 43	36 - 45
8	X-RAY DIFFRACTION	8	A	A	44 - 51	46 - 53
9	X-RAY DIFFRACTION	9	A	A	52 - 61	54 - 63
10	X-RAY DIFFRACTION	10	A	A	62 - 68	64 - 70
11	X-RAY DIFFRACTION	11	A	A	69 - 73	71 - 75
12	X-RAY DIFFRACTION	12	A	A	74 - 79	76 - 81
13	X-RAY DIFFRACTION	13	A	A	80 - 89	82 - 91
14	X-RAY DIFFRACTION	14	A	A	90 - 97	92 - 99
15	X-RAY DIFFRACTION	15	A	A	98 - 110	100 - 112
16	X-RAY DIFFRACTION	16	A	A	111 - 118	113 - 120
17	X-RAY DIFFRACTION	17	A	A	119 - 131	121 - 133
18	X-RAY DIFFRACTION	18	A	A	132 - 136	134 - 138
19	X-RAY DIFFRACTION	19	A	A	137 - 141	139 - 143
20	X-RAY DIFFRACTION	20	A	A	142 - 147	144 - 149

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