PDB-6h4i: Usp28 catalytic domain apo

ID or keywords:

Entry

Database: PDB / ID: 6h4i

Title

Usp28 catalytic domain apo

Components

Ubiquitin carboxyl-terminal hydrolase 28

Keywords

HYDROLASE / Ubiquitin / Deubiquitinase / Usp / Cancer

Function / homology

Function and homology information

protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / protein deubiquitination / response to ionizing radiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cell population proliferation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.22 Å

Authors

Klemm, T.A. / Sauer, F. / Kisker, C.

Funding support

Germany, 1items

Citation

Journal: Mol.Cell / Year: 2019
Title: Differential Oligomerization of the Deubiquitinases USP25 and USP28 Regulates Their Activities.
Authors: Sauer, F. / Klemm, T. / Kollampally, R.B. / Tessmer, I. / Nair, R.K. / Popov, N. / Kisker, C.

History

Deposition	Jul 21, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 10, 2019	Group: Data collection / Database references Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2	May 15, 2019	Group: Data collection / Database references Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info Item: _citation.journal_volume / _citation.page_first / _pdbx_seq_map_depositor_info.one_letter_code_mod

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6h4i.cif.gz	390.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6h4i.ent.gz	335.5 KB	Display	PDB format
PDBx/mmJSON format	6h4i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6h4i_validation.pdf.gz	451.7 KB	Display	wwPDB validaton report
Full document	6h4i_full_validation.pdf.gz	463.3 KB	Display
Data in XML	6h4i_validation.xml.gz	32.1 KB	Display
Data in CIF	6h4i_validation.cif.gz	43.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h4/6h4i ftp://data.pdbj.org/pub/pdb/validation_reports/h4/6h4i	HTTPS FTP

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Related structure data

Related structure data	6h4hC 6h4jC 6h4kC C: citing same article (ref.)
Similar structure data	6hej-d 6hek-d 2hyb-d 6h4h-1 1izo-d Search similar-shape structures by Omokage search (details) 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	#60 - Dec 2004 Ubiquitin similarity (2) #234 - Jun 2019 MDM2 and Cancer similarity (1) #81 - Sep 2006 Elongation Factors similarity (1)

Deposited unit

A: Ubiquitin carboxyl-terminal hydrolase 28

C: Ubiquitin carboxyl-terminal hydrolase 28

hetero molecules

132 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ubiquitin carboxyl-terminal hydrolase 28

hetero molecules

C: Ubiquitin carboxyl-terminal hydrolase 28

defined by author&software
Evidence: light scattering, SEC MALS
132 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	105.538, 200.518, 207.244
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

#1: Protein	Ubiquitin carboxyl-terminal hydrolase 28 / Deubiquitinating enzyme 28 / Ubiquitin thioesterase 28 / Ubiquitin-specific-processing protease 28 Mass: 65812.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄

#1: Protein

Ubiquitin carboxyl-terminal hydrolase 28 / Deubiquitinating enzyme 28 / Ubiquitin thioesterase 28 / Ubiquitin-specific-processing protease 28

Mass: 65812.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1

#2: Chemical

ChemComp-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.17 Å³/Da / Density % sol: 70.47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M citric acid pH 5.0 0.8 M Ammonium Sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 27, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 3.22→49.59 Å / Num. obs: 25908 / % possible obs: 94.3 % / Redundancy: 13.8 % / B_iso Wilson estimate: 91.48 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.041 / Net I/σ(I): 15.2
Reflection shell	Resolution: 3.223→3.493 Å / Mean I/σ(I) obs: 1.3 / CC_1/2: 0.417 / R_pim(I) all: 0.562 / % possible all: 60.5

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Processing

Software

Name	Version	Classification
BUSTER	2.10.3	refinement
XDS		data reduction
STARANISO		data scaling
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.22→49.59 Å / Cor.coef. F_o:F_c: 0.947 / Cor.coef. F_o:F_c free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R_free Blow DPI: 0.361

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.196	1096	4.23 %	RANDOM
R_work	0.171	-	-	-
obs	0.172	25907	72.1 %	-

Displacement parameters

B_iso mean: 144.91 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.9547 Å²	0 Å²	0 Å²
2-	-	6.2962 Å²	0 Å²
3-	-	-	-2.3414 Å²

Refine analyze

Luzzati coordinate error obs: 0.38 Å

Refinement step

Cycle: 1 / Resolution: 3.22→49.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7308	0	10	0	7318

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.009	7492	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.04	10165	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		3436	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes
X-RAY DIFFRACTION	t_gen_planes		1271	HARMONIC	5
X-RAY DIFFRACTION	t_it		7492	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	2.29
X-RAY DIFFRACTION	t_other_torsion	3.46
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		941	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		8352	SEMIHARMONIC	4

LS refinement shell

Resolution: 3.22→3.35 Å / Total num. of bins used: 13

	R_factor	Num. reflection	% reflection
R_free	0.3496	-	3.14 %
R_work	0.235	278	-
all	0.2381	287	-
obs	-	-	7.12 %

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	7.0827	-0.8604	0.8725	5.0984	0.5486	4.6783	-0.405	-0.2149	1.2774	0.3901	0.6277	-0.582	-0.7042	0.3411	-0.2227	0.0062	-0.0848	0.0641	-0.3354	-0.0567	-0.1094	-34.4308	-29.6474	-5.0916
2	14.3332	2.9836	6.2249	3.6446	2.5948	7.6157	-0.434	-0.3465	1.9099	0.4304	0.5488	-0.5172	-1.0647	0.3898	-0.1147	-0.0875	-0.0577	-0.0488	-0.5627	-0.019	0.2834	-35.1668	-26.4091	-5.9152
3	4.1386	8.9708	-11.1642	3.4042	11.3625	0.1214	0.0159	0.1413	0.1889	-0.2356	0.013	-0.7476	0.2855	0.6296	-0.0289	-0.6439	-0.0826	-0.0278	0.0039	-0.0698	0.6355	-20.5353	-32.2499	-6.4108
4	0	5.187	-1.9086	5.1743	-0.5643	1.1899	-0.0964	-0.8561	1.5795	0.0371	-0.0341	-0.2357	-0.0234	0.4065	0.1305	0.0733	-0.1308	-0.2322	0.3655	-0.2987	0.0754	-22.0879	-37.369	6.955
5	5.548	8.9237	3.9682	2.9711	-4.1661	0	-0.0894	0.5486	0.5032	-0.205	-0.2634	-0.2865	-0.8735	1.3208	0.3529	0.0413	-0.0704	0.0294	0.5719	-0.0616	-0.3658	-2.156	-51.6016	-4.2478
6	8.9763	-0.4762	-0.0929	4.5776	-0.8598	10.7128	-0.0182	0.9366	0.7562	-0.6733	-0.0624	-0.7801	-0.3592	1.1699	0.0806	-0.2473	-0.0551	0.1479	0.3848	0.0172	-0.3655	-15.2887	-49.642	-15.8105
7	0.7564	-0.9329	-1.0001	2.7341	1.4556	1.0789	-0.2778	-0.41	-0.0879	0.1223	0.597	-0.6065	0.6016	0.7396	-0.3193	0.1105	0.2192	0.1375	0.0858	-0.0389	-0.2364	-12.0255	-66.3019	-19.0877
8	9.6417	2.2508	-0.8127	15.9472	1.9179	16.8575	0.311	0.9553	0.5346	-1.1021	0.0288	0.1188	-1.2033	-0.3848	-0.3399	-0.0169	0.2083	0.1589	-0.2357	0.1223	-0.4004	-6.8202	-82.7838	-58.6964
9	1.2566	-0.7121	-0.689	0.8614	5.4942	12.2836	-0.0606	-0.132	-0.1684	0.4465	-0.3803	0.628	0.5652	-0.5886	0.4409	0.1647	0.0366	0.1206	-0.0696	0.0146	-0.2455	-10.5939	-86.3019	-42.6349
10	3.0561	-1.9305	1.3734	0	-2.0853	2.778	-0.2127	0.1828	-0.6339	0.4255	0.1922	0.3132	0.721	-0.1226	0.0205	0.0894	0.0445	0.1154	0.1193	-0.0318	-0.2029	-24.6705	-60.9344	-10.3934
11	0	9.8867	-7.5901	1.689	-7.1911	1.5692	-0.066	0.7833	0.5465	-0.6255	-0.1465	-0.366	-0.8051	0.536	0.2124	0.2822	-0.1225	0.0168	0.4689	0.2943	-0.0396	-27.9839	-35.4329	-24.0995
12	10.0821	-4.5692	-2.0923	4.4202	0.9702	5.0239	0.0092	1.0596	0.427	-0.4253	-0.0442	-0.4332	0.3834	0.0703	0.0351	-0.1805	-0.1138	0.1214	-0.2445	0.0839	-0.6751	-34.5104	-46.3372	-17.611
13	2.5297	-10.227	-0.5617	0	-8.2887	0	0.0345	-0.0702	-0.8674	-0.0586	-0.1169	-0.3415	0.2998	0.6823	0.0824	0.8218	-0.0456	-0.1481	0.0569	0.0472	0.751	-37.6312	-53.6625	-0.0581
14	0	-6.1115	0.436	6.1883	-13.0031	19.2908	-0.0917	-0.2737	-0.5761	0.7418	-0.0829	0.5076	0.495	-0.802	0.1747	0.1015	0.002	0.19	0.0115	-0.2661	-0.0917	-45.699	-36.7892	4.044
15	0.0751	-0.6638	-5.2268	5.5208	-0.6468	0	0.189	0.5456	1.7741	-0.3126	0.2304	0.382	-1.1561	0.0037	-0.4194	0.104	0.0018	0.0974	-0.4102	0.1894	0.4456	-52.6289	-20.621	-7.2675
16	5.8641	0.6071	-3.235	18.6974	-1.4261	2.9531	0.002	0.4596	-1.5172	-0.7216	-0.2183	-1.0128	0.0939	-0.1344	0.2163	-0.0105	-0.2512	0.5306	-0.4385	-0.2606	0.5326	-52.8053	-86.6957	-22.0526
17	9.9323	3.135	-3.8647	6.0446	2.3034	7.8196	-0.3252	0.0092	-0.7582	-0.6595	-0.5103	0.3744	0.5705	-1.1925	0.8355	0.1536	-0.4321	0.555	-0.7299	-0.3644	0.4496	-57.9591	-85.9573	-23.8098
18	0.0097	7.436	6.9283	0.1479	8.3038	0.3249	-0.0674	-0.8452	-1.4917	0.0831	0.6614	0.3914	-0.1118	-0.4726	-0.594	0.0489	-0.2539	0.4867	-0.2551	0.2356	0.3106	-64.1947	-80.7184	-6.2988
19	4.4058	7.4579	2.908	0	5.4903	2.8331	-0.0498	0.3098	0.6478	-0.1956	-0.0729	1.0607	-0.6463	-1.5722	0.1226	-0.1875	-0.1739	0.3655	0.2856	-0.2056	0.3325	-75.5863	-58.1764	-11.4255
20	9.4062	-1.4825	-0.4861	14.9162	2.9198	15.1524	0.0635	0.8906	-0.5887	-1.3918	-0.6003	0.9855	-0.4241	-1.8593	0.5368	-0.4674	-0.1194	0.0956	-0.1168	-0.0265	-0.5964	-62.7049	-59.5509	-20.5891
21	0	12.3045	8.0861	0	-6.1968	1.2246	0.0596	0.1701	-0.4666	-0.3025	-0.0412	1.0816	-0.2555	-0.1091	-0.0184	1.0351	0.0672	0.15	0.8749	-0.1795	0.5096	-64.843	-60.1263	-37.5557
22	7.8112	-5.4623	0.7254	10.0795	8.8099	1.2162	0.0223	0.013	0.3656	0.4582	0.0561	-0.4722	-0.1734	-0.3583	-0.0783	-0.0228	-0.0459	0.2754	-0.4604	0.0939	-0.2475	-55.0061	-56.4993	-16.5903
23	0.0942	0.4747	-1.3949	8.599	-8.9561	12.0732	0.0298	-0.0123	-0.0182	-0.2459	0.2147	0.2664	0.3356	-0.3967	-0.2445	-0.1656	-0.1584	-0.0852	-0.0847	0.0616	-0.2016	-56.145	-23.8727	-37.5034
24	1.2971	3.71	2.3405	0.0199	-2.7949	8.799	-0.2722	0.0884	-0.1231	0.3627	-0.3351	-0.5324	-0.1697	-0.265	0.6072	-0.3592	-0.1937	0.24	-0.2182	0.1003	-0.1082	-51.2136	-55.1153	-13.8283
25	0	4.7535	9.3217	0	-6.2855	0	0.0005	0.6322	-0.1045	-0.6994	-0.0606	0.6041	0.1655	-0.75	0.0601	0.6368	-0.3028	0.4459	0.5126	-0.4709	0.0962	-55.5595	-72.3587	-36.8993
26	9.2395	-3.7862	-3.8524	13.313	2.0194	4.3872	-0.1353	0.4017	-0.5914	-1.7414	-0.2567	-1.684	0.3033	-0.1739	0.392	0.1362	-0.2597	0.5961	-0.4408	-0.0476	-0.0188	-46.5462	-68.2844	-26.2396
27	0	0.9156	-2.9425	0.1088	-0.1973	0	-0.0006	-0.1075	-0.126	0.1205	-0.0276	-0.1617	-0.0172	0.2489	0.0282	0.2115	0.12	-0.2145	-0.1343	-0.0003	0.2961	-39.3051	-88.8025	-11.8908
28	7.3277	-6.6325	0.0001	2.9809	4.3198	1.0173	0.1976	0.5053	-0.4427	0.2733	-0.0713	0.322	0.1546	0.6222	-0.1263	0.0617	-0.2363	0.6175	-0.9545	-0.0927	0.9498	-38.5216	-99.6694	-27.5578

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{A\|148 - 211}
2	X-RAY DIFFRACTION	2	{A\|212 - 248}
3	X-RAY DIFFRACTION	3	{A\|249 - 270}
4	X-RAY DIFFRACTION	4	{A\|271 - 294}
5	X-RAY DIFFRACTION	5	{A\|295 - 312}
6	X-RAY DIFFRACTION	6	{A\|313 - 385}
7	X-RAY DIFFRACTION	7	{A\|386 - 430}
8	X-RAY DIFFRACTION	8	{A\|431 - 534}
9	X-RAY DIFFRACTION	9	{A\|535 - 571}
10	X-RAY DIFFRACTION	10	{A\|572 - 589}
11	X-RAY DIFFRACTION	11	{A\|590 - 603}
12	X-RAY DIFFRACTION	12	{A\|604 - 652}
13	X-RAY DIFFRACTION	13	{A\|653 - 663}
14	X-RAY DIFFRACTION	14	{A\|664 - 674}
15	X-RAY DIFFRACTION	15	{A\|675 - 705}
16	X-RAY DIFFRACTION	16	{C\|149 - 211}
17	X-RAY DIFFRACTION	17	{C\|212 - 270}
18	X-RAY DIFFRACTION	18	{C\|271 - 294}
19	X-RAY DIFFRACTION	19	{C\|295 - 312}
20	X-RAY DIFFRACTION	20	{C\|313 - 369}
21	X-RAY DIFFRACTION	21	{C\|370 - 385}
22	X-RAY DIFFRACTION	22	{C\|386 - 400}
23	X-RAY DIFFRACTION	23	{C\|401 - 571}
24	X-RAY DIFFRACTION	24	{C\|572 - 589}
25	X-RAY DIFFRACTION	25	{C\|590 - 603}
26	X-RAY DIFFRACTION	26	{C\|604 - 663}
27	X-RAY DIFFRACTION	27	{C\|664 - 673}
28	X-RAY DIFFRACTION	28	{C\|674 - 705}

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