PDB-3s8i: The retroviral-like protease (RVP) domain of human DDI1

ID or keywords:

Entry

Database: PDB / ID: 3s8i

Title

The retroviral-like protease (RVP) domain of human DDI1

Components

Protein DDI1 homolog 1

Keywords

HYDROLASE / PROTEASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / retropepsin-like domain / PROTEIN TURNOVER

Function / homology

Function and homology information

regulation of DNA stability / cellular response to hydroxyurea / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / proteasomal protein catabolic process / regulation of protein stability / aspartic-type endopeptidase activity
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

molecular replacement / Resolution: 1.7 Å

Authors

Walker, J.R. / Asinas, A. / Dong, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)

Citation

Journal: To be Published
Title: Retropepsin-Like Domain of Human DDI1
Authors: Walker, J.R. / Asinas, A. / Dong, A. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)

History

Deposition	May 28, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 6, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3s8i.cif.gz	124.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3s8i.ent.gz	98.7 KB	Display	PDB format
PDBx/mmJSON format	3s8i.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/s8/3s8i ftp://data.pdbj.org/pub/pdb/validation_reports/s8/3s8i	HTTPS FTP

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Related structure data

Related structure data	2ilaS S: Starting model for refinement
Similar structure data	6ifp-d 5n91-d 4uxa-2 5mh3-7 6mld-d 6dkq-d 6b15-1 6oi4-2 2lao-d 5mh3-5 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

Deposited unit

A: Protein DDI1 homolog 1

B: Protein DDI1 homolog 1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	80.981, 41.040, 88.975
Angle α, β, γ (deg.)	90.00, 107.62, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 2 molecules AB

#1: Protein	Protein DDI1 homolog 1 Mass: 16415.049 Da / Num. of mol.: 2 / Fragment: unp residues 239-367 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DDI1 / Plasmid: PET28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8WTU0

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Non-polymers , 5 types, 181 molecules

#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-UNX / UNKNOWN ATOM OR ION Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.15 Å³/Da / Density % sol: 42.73 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 21% PEG3350, 0.2 M AMMONIUM PHOSPHATE, 0.1 M BIS-TRIS, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 / Wavelength: 1.54178 Å

Detector

Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 26, 2011 / Details: OSMIC MIRRORS

Radiation

Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.5418	1
2	1.54178	1

Reflection

Resolution: 1.7→30 Å / Num. all: 30254 / Num. obs: 30254 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / R_sym value: 0.043 / Net I/σ(I): 52.372

Reflection shell

Resolution: 1.7→1.73 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 7.74 / Num. unique all: 1112 / R_sym value: 0.314 / % possible all: 73.4

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

molecular replacement
Starting model: pdb entry 2ILA

2ila

Resolution: 1.7→28.27 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.956 / SU B: 3.285 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19871	1499	5 %	RANDOM
R_work	0.17573	-	-	-
obs	0.17686	28725	97.65 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 27.812 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.42 Å²	0 Å²	-0.59 Å²
2-	-	0.65 Å²	0 Å²
3-	-	-	-0.59 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→28.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1891	0	27	175	2093

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	2050
X-RAY DIFFRACTION	r_angle_refined_deg	1.457	1.977	2767
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.303	5	263
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.323	23.412	85
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.887	15	384
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.444	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	312
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	1510
X-RAY DIFFRACTION	r_mcbond_it	0.757	1.5	1280
X-RAY DIFFRACTION	r_mcangle_it	1.338	2	2071
X-RAY DIFFRACTION	r_scbond_it	2.473	3	770
X-RAY DIFFRACTION	r_scangle_it	3.645	4.5	695

LS refinement shell

Resolution: 1.7→1.744 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.31	88	-
R_work	0.299	1631	-
obs	-	-	75.83 %

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	4.7447	0.4756	1.3447	2.028	-0.9232	6.2401	-0.0177	0.0914	0.013	-0.0974	0.1157	0.1177	0.1026	-0.4418	-0.098	0.0765	-0.0117	0.0063	0.0871	-0.0058	0.0886	0.8054	14.6165	-12.6036
2	5.2146	-1.1804	0.6032	4.7153	1.6129	3.6101	0.0018	-0.165	-0.0737	0.1261	0.0578	-0.1359	-0.0673	-0.0682	-0.0596	0.0713	-0.0002	0.0005	0.0808	0.0165	0.0874	10.3694	17.585	1.9939
3	1.5103	0.3172	-2.2992	0.9908	-1.0454	8.2257	-0.0147	0.017	0.0514	-0.0744	0.0637	0.0243	-0.0625	-0.0669	-0.049	0.0677	0.0092	-0.0039	0.0843	-0.0017	0.0906	5.1194	18.9755	-11.4274
4	2.2746	2.5199	5.7776	6.2392	5.4671	15.3287	-0.2812	0.1927	0.0736	-0.4809	0.1371	-0.0101	-0.901	0.4401	0.1441	0.1759	0.0041	0.0269	0.1261	0.029	0.1127	11.1785	26.5081	-15.5835
5	2.9974	1.0101	0.9094	3.0464	-2.1621	4.4453	0.1073	-0.0991	0.0976	0.1251	-0.0158	0.1149	-0.1012	-0.0573	-0.0915	0.0773	0.0003	0.0135	0.0671	-0.0129	0.0934	8.6176	27.1203	1.272
6	3.1556	2.4665	0.8575	6.1655	-0.5106	5.9369	-0.0123	0.0342	0.1212	-0.0601	-0.1176	-0.0029	-0.2419	0.282	0.1298	0.0677	-0.0222	-0.0135	0.0639	-0.0037	0.1288	18.9103	33.7981	-1.6608
7	28.6928	-9.9899	12.5036	3.6203	-4.029	6.2926	1.0407	2.5646	-0.4964	-0.5896	-0.7995	0.224	-0.0369	1.2624	-0.2412	0.4366	-0.052	-0.1046	0.3508	0.0997	0.2937	12.6483	37.3583	-11.8836
8	2.5176	-1.0739	-1.4517	6.0851	0.5225	1.5355	0.0567	0.1313	0.1127	-0.1575	0.0059	0.1195	-0.2122	0.1147	-0.0626	0.1096	-0.0225	-0.0021	0.0719	0.0046	0.1318	14.5083	33.1279	-6.6387
9	3.617	2.9895	1.5717	3.6873	-0.2328	2.6142	0.116	-0.0446	-0.1622	0.0038	-0.0243	-0.1246	0.156	-0.0395	-0.0917	0.0826	0.0137	-0.0031	0.0714	0.0063	0.1233	15.0422	13.8747	-3.4384
10	5.1972	0.5296	-2.8786	14.446	-11.1195	9.7457	0.2513	-0.2401	-0.1497	-0.1681	-0.4743	-0.1516	0.0082	0.4912	0.2231	0.098	-0.0064	0.0025	0.1201	-0.0006	0.1784	19.1206	14.9828	-5.0685
11	13.1541	-6.1815	-1.2276	7.6745	-0.8082	4.3643	0.0492	-0.0358	0.2954	0.0289	0.1062	0.0515	-0.2256	-0.0511	-0.1554	0.0767	-0.0081	-0.0039	0.0527	0.0089	0.107	11.3291	30.2619	-6.7612
12	6.7754	4.58	-2.2044	8.9135	-2.5709	7.1055	-0.1676	0.5293	0.5976	0.0226	0.4736	0.48	0.0576	-0.8352	-0.3061	0.0293	0.0225	-0.0194	0.2064	0.0477	0.1646	2.1412	27.6318	-6.7406
13	5.3955	-0.9977	-4.733	1.0275	2.7705	8.4178	0.0607	0.011	-0.0288	-0.0519	0.0409	-0.0553	-0.1315	0.0655	-0.1016	0.0974	-0.0119	-0.0026	0.0714	-0.0049	0.0951	11.8334	21.0699	-13.2107
14	5.8294	3.0717	0.0963	4.0671	1.1183	2.1601	0.0421	0.0904	-0.1563	-0.0706	0.0974	-0.1509	0.1525	0.2282	-0.1394	0.0797	0.027	0.001	0.0818	-0.0433	0.0779	13.5137	12.155	-17.829
15	9.0485	-0.6696	-0.4069	1.9717	-2.3956	4.3088	0.078	-0.1588	-0.2913	-0.046	-0.1365	-0.0573	0.242	0.3997	0.0585	0.0972	0.0181	-0.0056	0.0859	-0.0151	0.0977	12.0279	7.6057	-12.2614
16	8.0937	-6.1604	-4.2993	7.1959	6.3137	6.877	0.0463	-0.0145	-0.2044	0.0111	-0.0988	-0.0163	0.0213	-0.4586	0.0525	0.1019	-0.0271	0.0086	0.1599	-0.0092	0.1203	-3.368	12.8936	-7.9429
17	2.1751	-1.1809	0.572	2.0352	2.747	6.8607	0.1134	0.0277	0.2204	-0.4703	0.3489	-0.3545	-0.8433	0.7954	-0.4622	0.2337	-0.146	0.0772	0.225	-0.038	0.1021	14.4707	26.0483	-23.1046
18	6.6346	0.0792	3.8114	2.7043	-0.5033	6.0976	-0.0664	0.637	-0.0736	-0.254	0.1962	0.1222	-0.1558	0.2226	-0.1298	0.1493	-0.0185	0.005	0.2219	-0.0198	0.0126	5.061	17.0465	-41.3824
19	0.3658	0.4883	-0.5889	1.6792	-2.5681	16.0231	0.0341	0.1706	0.0332	-0.1946	0.0441	0.1162	-0.0597	0.1462	-0.0782	0.1424	0.0102	-0.0029	0.1425	-0.0045	0.0568	6.3716	20.6555	-29.6041
20	6.6845	-1.8549	9.4089	6.5872	1.9844	17.1107	-0.031	-0.6517	-0.0014	-0.0114	-0.1017	0.3193	0.0338	-1.3092	0.1327	0.0932	0.007	-0.0077	0.2219	0.0136	0.0795	-3.4407	19.6184	-23.9741
21	1.7108	-1.4096	3.2211	7.3592	-4.1728	13.6623	0.0136	0.1622	0.0709	-0.1236	0.2338	0.2602	-0.2585	-0.2737	-0.2474	0.1433	0.0117	-0.037	0.1875	0.0709	0.0524	-3.1117	25.7064	-38.2053
22	14.5995	2.7544	-3.5382	4.2277	-2.575	6.1945	0.1098	0.6374	-0.1549	-0.5448	0.1549	0.2844	0.0543	-0.2282	-0.2647	0.2061	0.0138	-0.0821	0.2247	0.0458	0.0612	-7.2826	20.8336	-42.7941
23	31.139	8.9039	-11.2961	18.6867	5.4098	28.9793	-0.0318	-1.0827	0.4878	0.8943	-0.108	2.1474	1.5892	0.0876	0.1398	0.2233	0.1635	0.064	0.4424	0.0827	0.3236	-16.4484	23.3962	-33.1829
24	6.118	-2.1355	-2.539	8.506	3.1054	5.2936	-0.1431	0.175	0.0366	0.0923	0.2535	0.5533	-0.0381	-0.1294	-0.1104	0.1133	0.0387	-0.0459	0.245	0.075	0.1063	-10.2109	20.1815	-34.1389
25	8.2634	1.4269	1.8579	2.7552	1.3891	5.8316	0.0882	0.394	-0.5654	-0.1982	0.1528	0.2803	0.3761	0.0366	-0.241	0.185	-0.0167	-0.0353	0.2182	-0.0744	0.1379	4.5773	9.8518	-38.3949
26	2.9094	-3.446	-2.0816	7.7147	0.9247	2.2665	-0.224	0.2595	-0.106	0.2982	0.3002	0.3708	0.0676	-0.3309	-0.0762	0.153	-0.0511	-0.0505	0.2428	-0.0313	0.1135	-3.9211	15.5529	-34.7717
27	35.9714	-3.3459	-13.288	3.9544	3.0239	5.7879	1.4569	-0.4674	3.5114	-0.5576	-0.1035	-0.7166	-0.7403	0.0496	-1.3534	0.7357	-0.1191	-0.1258	0.286	0.0889	0.5367	0.5001	29.3817	-33.4589
28	4.379	3.8495	-6.3977	11.3078	-14.194	18.618	0.0343	0.0938	0.0109	0.031	0.1836	0.2063	-0.0625	-0.2376	-0.2179	0.1312	0.0168	-0.0286	0.1535	-0.0044	0.0508	1.4835	19.192	-28.8427
29	7.1218	1.6442	-1.1311	11.6991	2.587	9.3506	0.1033	-0.0457	-0.3014	-0.5091	0.032	0.4709	0.2632	-0.5446	-0.1353	0.0944	-0.0304	-0.0429	0.1659	0.0041	0.0811	-1.616	11.2668	-25.5473
30	11.2998	0.7965	1.573	1.7417	-0.027	3.0463	0.0487	0.152	-0.4293	-0.1679	0.0346	-0.13	0.2942	0.1509	-0.0833	0.1001	0.0285	0.0047	0.0848	-0.0427	0.0459	10.8817	9.2983	-24.7758
31	4.8897	6.0264	-1.1808	11.1953	-0.8412	5.085	-0.0834	0.4619	-0.3456	-0.2208	0.1341	-0.2719	0.434	0.1388	-0.0507	0.1408	0.0382	-0.0002	0.1457	-0.0748	0.0724	11.0382	8.9537	-30.7572
32	39.5368	-7.7292	13.1456	19.8772	-13.0854	18.8177	-0.041	0.2418	1.3168	0.1762	0.1512	-0.0241	-0.8535	-0.2222	-0.1101	0.1852	-0.0591	0.0896	0.3097	-0.0024	0.0909	16.5059	24.5988	-33.3773

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	241 - 247
2	X-RAY DIFFRACTION	2	A	248 - 254
3	X-RAY DIFFRACTION	3	A	255 - 261
4	X-RAY DIFFRACTION	4	A	262 - 267
5	X-RAY DIFFRACTION	5	A	268 - 278
6	X-RAY DIFFRACTION	6	A	279 - 285
7	X-RAY DIFFRACTION	7	A	286 - 292
8	X-RAY DIFFRACTION	8	A	296 - 304
9	X-RAY DIFFRACTION	9	A	305 - 311
10	X-RAY DIFFRACTION	10	A	312 - 316
11	X-RAY DIFFRACTION	11	A	317 - 322
12	X-RAY DIFFRACTION	12	A	323 - 327
13	X-RAY DIFFRACTION	13	A	328 - 335
14	X-RAY DIFFRACTION	14	A	336 - 347
15	X-RAY DIFFRACTION	15	A	348 - 360
16	X-RAY DIFFRACTION	16	A	361 - 367
17	X-RAY DIFFRACTION	17	B	221 - 245
18	X-RAY DIFFRACTION	18	B	246 - 254
19	X-RAY DIFFRACTION	19	B	255 - 261
20	X-RAY DIFFRACTION	20	B	262 - 266
21	X-RAY DIFFRACTION	21	B	267 - 274
22	X-RAY DIFFRACTION	22	B	275 - 283
23	X-RAY DIFFRACTION	23	B	284 - 288
24	X-RAY DIFFRACTION	24	B	297 - 305
25	X-RAY DIFFRACTION	25	B	306 - 312
26	X-RAY DIFFRACTION	26	B	313 - 321
27	X-RAY DIFFRACTION	27	B	322 - 327
28	X-RAY DIFFRACTION	28	B	328 - 332
29	X-RAY DIFFRACTION	29	B	333 - 337
30	X-RAY DIFFRACTION	30	B	338 - 348
31	X-RAY DIFFRACTION	31	B	349 - 361
32	X-RAY DIFFRACTION	32	B	362 - 367

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The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 181 molecules

-Experimental details

-Experiment

-Sample preparation

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+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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+Jul 12, 2017. Major update of PDB

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Movie

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Structure viewers

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This page

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This web site

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 181 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi