PDB-2esq: Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly

ID or keywords:

Entry

Database: PDB / ID: 2esq

Title

Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly

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: 1.44 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	2esq.cif.gz	50.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2esq.ent.gz	35.6 KB	Display	PDB format
PDBx/mmJSON format	2esq.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/2esq ftp://data.pdbj.org/pub/pdb/validation_reports/es/2esq	HTTPS FTP

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Related structure data

Related structure data	2eskSC 2esoC 2espC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4gpr-d 2esk-d 1jbb-1 1s3d-d 2c4p-1 2eso-d 3rpg-2 2c4p-2 5egg-d 1sd8-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

16.9 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)	47.514, 49.295, 62.617
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: 16853.332 Da / Num. of mol.: 1 / Mutation: S94G 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.: 148 / 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: 16853.332 Da / Num. of mol.: 1 / Mutation: S94G
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.: 148 / 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: 0.97881 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: 0.97881 Å / Relative weight: 1
Reflection	Resolution: 1.44→50 Å / Num. obs: 26980 / % possible obs: 98.7 % / Redundancy: 6.7 % / R_merge(I) obs: 0.053 / Net I/σ(I): 34.2
Reflection shell	Resolution: 1.44→1.49 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.544 / Mean I/σ(I) obs: 2.5

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Phasing

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.5 Å	38.73 Å
Translation	2.5 Å	38.73 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: 1.44→38.72 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.959 / SU B: 2.548 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2047	1369	5.1 %	RANDOM
R_work	0.17334	-	-	-
obs	0.17495	25571	98.72 %	-

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: 22.04 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.82 Å²	0 Å²	0 Å²
2-	-	-0.28 Å²	0 Å²
3-	-	-	1.1 Å²

Refinement step

Cycle: LAST / Resolution: 1.44→38.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1185	0	0	148	1333

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.029	0.022	1263
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.369	1.97	1734
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	14.058	5	163
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.218	23.519	54
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.772	15	211
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.898	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.154	0.2	189
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	980
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	617
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.324	0.2	882
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	92
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	0.245	0.2	57
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.18	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	1.568	1.5	806
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	2.051	2	1277
X-RAY DIFFRACTION	r_scbond_it	3.379	3	536
X-RAY DIFFRACTION	r_scangle_it	5.039	4.5	449
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 (%)
1.44-1.477	0.268	93	0.216	1791	1981	95.103
1.477-1.518	0.244	99	0.212	1786	1930	97.668
1.518-1.562	0.226	108	0.205	1738	1874	98.506
1.562-1.609	0.211	81	0.186	1725	1828	98.797
1.609-1.662	0.236	69	0.184	1703	1784	99.327
1.662-1.72	0.195	91	0.171	1620	1721	99.419
1.72-1.785	0.221	78	0.187	1571	1662	99.218
1.785-1.858	0.249	74	0.19	1521	1602	99.563
1.858-1.94	0.203	70	0.191	1460	1535	99.674
1.94-2.035	0.235	63	0.182	1412	1480	99.662
2.035-2.145	0.176	82	0.167	1334	1421	99.648
2.145-2.274	0.194	70	0.16	1250	1324	99.698
2.274-2.431	0.166	63	0.173	1196	1265	99.526
2.431-2.624	0.184	77	0.179	1091	1177	99.235
2.624-2.874	0.215	63	0.179	1017	1085	99.539
2.874-3.211	0.187	59	0.169	926	992	99.294
3.211-3.703	0.205	44	0.154	811	889	96.175
3.703-4.525	0.18	35	0.149	716	756	99.339
4.525-6.356	0.217	27	0.179	572	609	98.358
6.356-38.72	0.278	23	0.183	331	375	94.4

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	13.7089	3.4862	0.153	9.2475	-0.2201	4.9769	0.2028	0.0386	0.0953	-0.4005	-0.2002	-0.8135	0.1547	0.1242	-0.0026	-0.0142	0.0444	0.0539	-0.0436	0.0194	0.0661	37.427	-7.123	58.996
2	5.8848	2.2248	2.557	6.732	1.6557	3.9725	0.1241	0.3091	0.1039	-0.5169	-0.0864	-0.3576	0.0596	0.2155	-0.0377	0.0317	0.0415	0.0568	-0.0055	0.013	-0.0049	31.073	-5.38	55.17
3	20.5385	9.2021	4.5609	24.8298	-2.8093	10.3614	-0.7823	0.8927	0.2529	-1.6796	0.6609	1.061	0.4499	0.1149	0.1214	0.1209	-0.0225	-0.0589	-0.0341	-0.0027	-0.0304	23.401	-6.748	50.363
4	17.3046	0.5276	0.4077	13.5292	1.927	0.2809	-0.6041	0.5967	-0.7884	-0.3534	0.5599	0.594	-0.3664	0.35	0.0442	0.0199	-0.0249	0.0017	0.0877	-0.0111	-0.0203	16.007	-2.78	55.996
5	6.3294	6.8	-2.1237	10.2581	-2.6533	5.2785	-0.1643	0.1593	0.0776	-0.2379	0.1156	-0.2673	-0.143	0.0793	0.0487	0.0355	-0.0051	0.0487	-0.0157	-0.0042	0.0617	30.594	6.295	57.298
6	6.5841	-2.2888	0.6386	4.4899	-2.4117	4.4093	-0.0767	-0.0136	0.2794	-0.0911	0.1164	-0.5449	0.1563	0.1953	-0.0397	-0.0058	0.0021	0.0203	-0.0144	-0.0164	0.0321	30.719	2.114	60.736
7	13.8547	4.5553	0.6194	4.0216	0.3843	1.043	-0.1033	0.581	0.174	-0.1972	0.1514	0.1824	-0.0065	-0.04	-0.0481	-0.0021	-0.0078	-0.0301	0.0166	0.0032	-0.0314	10.345	-0.418	60.015
8	7.3822	1.8453	-0.0984	3.8143	-0.6179	2.0009	-0.0527	0.3387	0.4285	-0.1175	0.1166	0.3357	0.0227	-0.0098	-0.0639	-0.0123	0.0124	-0.0274	-0.0119	0.0124	0.0096	8.106	3.002	62.811
9	5.6552	-4.3713	-0.5819	5.7926	0.6724	0.2272	-0.0702	-0.1962	0.2017	0.1269	0.1794	-0.388	0.0578	0.0886	-0.1092	-0.0192	0.0064	-0.0249	0.0277	-0.0124	0.0055	30.243	-2.283	65.6
10	24.6554	-24.0605	-1.134	24.1783	1.8044	1.3689	-0.5055	-0.2929	0.433	0.7047	0.4685	-0.5153	0.1498	0.119	0.037	0.0074	0.0278	-0.0145	0.0281	-0.0106	-0.0132	29.034	-5.304	69.18
11	6.8769	-1.508	-1.9862	2.9681	-2.7647	4.4569	-0.1494	-0.3125	0.6577	0.1621	0.2041	-0.1382	-0.1612	-0.0092	-0.0547	0.0119	0.0179	-0.0227	0.008	-0.0427	0.0496	13.536	6.011	69.257
12	6.1583	-1.0464	-0.2987	0.2706	0.6149	3.4447	0.056	-0.2931	-0.0512	0.2293	-0.019	0.1161	0.099	0.0966	-0.037	0.0289	0.0105	0.0187	0.0389	-0.0062	-0.0488	10.341	-0.389	74.692
13	7.783	-7.076	-4.2452	15.0881	3.6471	4.4398	-0.1695	-0.3501	-0.1079	0.3379	0.0851	-0.2383	0.1564	0.0915	0.0844	-0.024	0.0132	-0.0237	0.042	0.009	-0.0937	19.08	-3.321	73.347
14	5.5227	-2.9939	0.254	4.4181	3.4152	9.6462	-0.3191	-0.4583	-0.3826	0.6497	0.2444	0.0898	0.5006	-0.0664	0.0747	0.0738	0.0308	0.0088	0.0073	0.0389	-0.0003	26.118	-12.71	69.697
15	8.7774	-1.6423	-1.7186	1.2349	0.8252	2.0423	-0.0863	0.0418	-0.0756	0.0887	0.0149	-0.0159	0.107	-0.0434	0.0714	-0.0007	-0.0038	0.0061	-0.0215	-0.0018	0.0006	17.478	-7.596	63.448
16	5.8452	1.1357	5.4192	6.3511	1.5928	32.1305	-0.0926	-0.3626	-0.1993	0.8765	-0.2639	-0.0568	0.4279	0.2797	0.3564	0.0804	-0.0218	0.0131	-0.0222	0.016	0.0247	9.57	-8.929	75.666
17	1.9669	-0.1233	-1.4202	0.7384	0.9856	2.1255	0.1772	-0.1028	-0.1713	0.4783	-0.2639	0.1999	0.3555	0.0795	0.0867	0.0745	-0.0636	0.0492	0.0569	-0.0181	-0.0427	3.396	-3.875	79.499
18	1.041	-4.0433	-0.0638	16.7192	-3.7526	15.7618	-0.1963	0.0713	0.154	0.4008	0.1167	1.2606	0.1972	-1.2202	0.0796	-0.0214	-0.0218	0.0858	0.058	-0.0673	0.0904	-2.862	-0.634	73.279
19	13.2591	3.216	-0.8271	12.278	0.548	6.431	0.0256	-0.4886	0.8895	0.5644	-0.1715	0.7309	-0.1854	-0.342	0.1459	-0.0112	0.035	0.0231	-0.0085	-0.0625	0.069	1.245	5.23	70.832
20	3.66	1.4046	0.4021	5.093	1.3443	2.5988	-0.1718	-0.0657	0.354	-0.0399	0.0446	0.1218	-0.0513	-0.1286	0.1272	-0.0231	0.0304	-0.0362	-0.0403	0.0037	0.0843	5.205	9.712	65.922

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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