PDB-2esk: Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type

ID or keywords:

Entry

Database: PDB / ID: 2esk

Title

Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type

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: 1.36 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	Aug 23, 2023	Group: Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2esk.cif.gz	52 KB	Display	PDBx/mmCIF format
PDB format	pdb2esk.ent.gz	37.2 KB	Display	PDB format
PDBx/mmJSON format	2esk.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/2esk ftp://data.pdbj.org/pub/pdb/validation_reports/es/2esk	HTTPS FTP

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Related structure data

Related structure data	2esoC 2espC 2esqC 1qcqS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1fzy-2 1sd8-d 2esq-d 2c4p-1 5egg-d 2esp-d 1j9b-d 1s3d-d 2c4p-2 1y6l-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	#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

16.9 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)	47.597, 49.372, 62.459
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: 16883.357 Da / Num. of mol.: 1 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 / Water Mass: 18.015 Da / Num. of mol.: 174 / 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: 16883.357 Da / Num. of mol.: 1
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 /

Water

Mass: 18.015 Da / Num. of mol.: 174 / 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 / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97897 Å / Relative weight: 1

Reflection

Resolution: 1.36→50 Å / Num. obs: 31496 / % possible obs: 97.2 % / Redundancy: 7 % / R_merge(I) obs: 0.041 / Χ²: 0.989

Reflection shell

Resolution (Å)	% possible obs (%)	Redundancy (%)	R_merge(I) obs	Num. measured obs	Χ²	Diffraction-ID
1.36-1.41	92.6	2.9	0.496	2954	0.789	1
1.41-1.47	98.5	4.8	0.464	3113	0.951	1
1.47-1.53	99.5	7.3	0.392	3189	1.031	1
1.53-1.61	99.3	7.8	0.278	3168	0.992	1
1.61-1.71	99.2	7.9	0.172	3197	0.909	1
1.71-1.85	99	7.9	0.121	3177	1.024	1
1.85-2.03	98.3	7.9	0.094	3169	0.973	1
2.03-2.33	97.4	7.8	0.058	3167	1.03	1
2.33-2.93	95.5	7.8	0.036	3144	1.058	1
2.93-50	93.2	7.4	0.021	3218	0.97	1

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Phasing

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.5 Å	30.04 Å
Translation	2.5 Å	30.04 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 1QCQ

1qcq

Resolution: 1.36→38.72 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.948 / WR_factor R_free: 0.246 / WR_factor R_work: 0.201 / SU B: 2.041 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2237	1590	5.054 %	RANDOM
R_work	0.1844	-	-	-
all	0.186	-	-	-
obs	0.186	31463	97.285 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 12.87 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.154 Å²	0 Å²	0 Å²
2-	-	-0.29 Å²	0 Å²
3-	-	-	0.444 Å²

Refinement step

Cycle: LAST / Resolution: 1.36→38.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1187	0	0	174	1361

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	1317
X-RAY DIFFRACTION	r_angle_refined_deg	1.872	1.96	1817
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.767	5	174
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.542	23.934	61
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.257	15	214
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.345	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.124	0.2	195
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1048
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	607
X-RAY DIFFRACTION	r_nbtor_refined	0.323	0.2	900
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.196	0.2	110
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.256	0.2	60
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.224	0.2	23
X-RAY DIFFRACTION	r_mcbond_it	0.994	1.5	833
X-RAY DIFFRACTION	r_mcangle_it	1.225	2	1332
X-RAY DIFFRACTION	r_scbond_it	2.116	3	559
X-RAY DIFFRACTION	r_scangle_it	3.187	4.5	475

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 (%)
1.359-1.395	0.29	96	0.244	2046	2356	90.917
1.395-1.433	0.229	116	0.23	2108	2282	97.458
1.433-1.474	0.272	109	0.205	2092	2221	99.1
1.474-1.52	0.211	118	0.185	2059	2187	99.543
1.52-1.569	0.207	121	0.186	1970	2103	99.429
1.569-1.624	0.19	84	0.176	1939	2034	99.459
1.624-1.686	0.193	83	0.182	1881	1975	99.443
1.686-1.754	0.221	103	0.174	1786	1905	99.16
1.754-1.832	0.227	87	0.176	1718	1831	98.58
1.832-1.921	0.23	77	0.183	1638	1736	98.79
1.921-2.025	0.25	67	0.181	1571	1668	98.201
2.025-2.148	0.212	83	0.171	1472	1603	97.006
2.148-2.295	0.184	77	0.171	1370	1476	98.035
2.295-2.479	0.255	65	0.189	1279	1398	96.137
2.479-2.714	0.214	77	0.2	1158	1285	96.109
2.714-3.032	0.233	70	0.205	1048	1181	94.666
3.032-3.498	0.226	58	0.18	926	1044	94.253
3.498-4.275	0.248	44	0.162	809	897	95.095
4.275-6.01	0.19	29	0.177	647	724	93.37
6.01-38.72	0.23	26	0.203	356	435	87.816

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	6.0534	1.5435	1.3764	3.4093	0.5536	4.72	0.232	-0.2528	0.2086	-0.1712	-0.1522	-0.141	0.2334	-0.2645	-0.0798	0.0747	-0.0005	0.0032	0.092	-0.0082	0.0323	30.3289	-6.8996	58.6722
2	12.5488	0.2182	4.2606	3.8161	-1.9753	2.5482	0.0575	-0.3149	-0.1052	-0.2804	-0.1116	-0.1029	0.0085	-0.1549	0.0541	0.0816	0.0096	0.0251	0.0397	0.0048	0.0614	30.0515	-6.0718	57.441
3	28.0807	6.8917	15.7895	15.4484	8.609	24.8793	-0.4679	0.2876	0.1468	0.3059	0.0905	0.4016	-0.0975	0.297	0.3775	0.1753	0.0273	-0.0498	0.0172	0.0196	0.0774	24.3436	-4.601	51.6056
4	19.052	7.1425	0.8402	9.6005	0.9274	3.1462	-0.0408	0.0234	0.1687	-0.0876	0.102	0.0053	0.0279	-0.1077	-0.0612	0.0775	0.0142	0.0228	0.0609	0.0065	-0.0025	22.9025	1.6408	57.579
5	10.5742	-2.0561	5.3469	5.0495	-0.601	4.9926	0.1147	-0.0791	0.0328	-0.1621	0.0681	0.0605	0.1572	0.0043	-0.1828	0.0537	-0.0176	0.0078	0.0318	0.0023	0.0666	26.7007	1.6181	59.7127
6	64.3952	14.9757	7.7806	8.9591	4.6818	2.4466	0.1017	-0.2766	-0.038	-0.2323	0.0766	0.0063	-0.1021	-0.0137	-0.1783	0.0343	-0.0135	0.0155	0.0389	0.0117	0.0095	18.0365	1.7393	60.6856
7	8.2455	4.6756	2.4304	14.1417	1.6901	1.4405	-0.1399	0.0241	0.0836	0.1199	-0.075	-0.1934	0.1102	-0.1736	0.2149	0.031	0.014	-0.0379	0.0362	0.0163	0.0746	6.2675	-0.0443	63.1063
8	8.8923	1.9595	-0.8576	6.3284	-1.2158	1.7382	-0.0115	0.0258	-0.0208	-0.0259	0.0262	0.0296	0.0031	0.0493	-0.0147	0.0191	0.0155	-0.002	0.0278	-0.0163	0.0361	9.772	0.4782	64.3341
9	21.4533	-10.3644	2.7893	6.7482	-0.3391	0.9904	0.112	-0.098	-0.1236	-0.0595	-0.0557	0.0928	0.097	0.0028	-0.0563	0.0324	-0.0167	0.0053	0.0606	0.0014	0.0474	24.4843	0.6583	64.8694
10	9.1746	-2.6723	-1.5987	6.5427	2.4721	8.3819	-0.0923	0.1176	0.0114	0.2485	0.1094	0.0073	0.0732	0.035	-0.0172	0.0252	0.0004	0.0081	0.0251	-0.0079	0.0492	30.6543	-7.9848	64.5652
11	14.0618	-6.3241	0.8376	4.3109	-1.04	0.3499	0.0082	-0.1699	-0.0153	-0.0847	-0.0383	0.0886	-0.0388	0.1017	0.0301	0.0592	0.0231	-0.0089	0.0708	-0.0191	0.0487	18.1922	0.8036	66.9655
12	6.9753	-1.0904	-1.9302	3.6884	-0.3118	6.7757	0.0313	-0.018	0.0097	0.0499	-0.0551	-0.0061	-0.0011	0.0273	0.0238	0.0792	0.0337	0.0093	0.0831	-0.0235	0.009	11.2371	-0.6063	72.5814
13	5.7181	-6.2546	-0.4727	16.6521	5.1757	9.2994	-0.4618	0.1198	-0.0636	0.1709	0.078	-0.1345	0.0647	-0.1595	0.3837	0.1083	0.0218	0.0042	0.1119	0.0296	0.0552	20.7367	-7.1833	71.9146
14	7.9362	-3.7698	0.1791	9.0873	1.5406	7.5567	0.0141	0.0594	0.0561	0.1988	0.0127	-0.0669	0.0736	0.0418	-0.0268	0.0398	0.0073	0.0062	0.0278	0.0088	0.0694	27.7033	-12.806	64.6522
15	16.206	-0.9282	-5.1307	1.7131	0.577	3.95	-0.0821	-0.0113	0.042	0.0395	0.0182	-0.0176	0.0395	-0.0409	0.0638	0.0306	0.0005	0.0052	0.0127	-0.0089	0.022	18.119	-7.5953	62.9702
16	4.8554	0.9857	5.245	9.4863	-4.8266	51.1414	-0.401	0.2498	0.1085	0.2078	-0.2451	-0.0136	-1.3188	1.5431	0.6461	0.085	-0.0653	-0.0062	0.13	-0.0269	0.1208	9.5707	-6.7528	66.9494
17	6.6562	3.0715	-0.906	4.3088	2.2478	6.6724	-0.09	0.009	0.0484	0.0411	0.0399	0.1728	0.0063	0.1193	0.0501	0.1227	-0.0147	0.0303	0.0658	-0.0266	0.0173	5.0292	-0.0037	77.5752
18	6.3361	-0.8379	1.0826	12.5091	-6.0849	5.6214	0.0708	0.1871	0.6722	-0.0231	-0.4655	-0.2295	0.1898	0.2185	0.3947	0.0702	0.0183	0.0703	0.1013	-0.0081	0.1989	1.6635	1.1732	69.9978
19	10.3897	3.3805	-3.1272	13.2499	-2.2341	5.9588	-0.1228	-0.0026	0.1277	0.2145	-0.061	-0.0077	0.0857	-0.0749	0.1839	0.0345	0.0259	-0.0037	0.0198	-0.0053	0.0985	4.0088	4.7943	67.8072
20	17.3362	1.0649	-2.5559	18.7254	0.2579	8.1722	-0.0087	0.084	0.1665	-0.0418	-0.0402	-0.2254	-0.15	0.009	0.0489	0.0229	0.0267	-0.0078	0.0279	0.0112	0.1325	6.7415	7.2458	65.2501

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Auth seq-ID	Label seq-ID
1	1	-1 - 7	1 - 9
2	2	8 - 12	10 - 14
3	3	13 - 17	15 - 19
4	4	18 - 29	20 - 31
5	5	30 - 33	32 - 35
6	6	34 - 38	36 - 40
7	7	39 - 44	41 - 46
8	8	45 - 50	47 - 52
9	9	51 - 59	53 - 61
10	10	60 - 64	62 - 66
11	11	65 - 73	67 - 75
12	12	74 - 84	76 - 86
13	13	85 - 89	87 - 91
14	14	90 - 97	92 - 99
15	15	98 - 110	100 - 112
16	16	111 - 117	113 - 119
17	17	118 - 130	120 - 132
18	18	131 - 135	133 - 137
19	19	136 - 141	138 - 143
20	20	142 - 147	144 - 149

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Yorodumi