PDB-5b5q: 1.7 Angstroms structure of ChlaDub1 from Chlamydia Trachomatis

ID or keywords:

Entry

Database: PDB / ID: 5b5q

Title

1.7 Angstroms structure of ChlaDub1 from Chlamydia Trachomatis

Components

(Membrane thiol protease) x 2

Keywords

HYDROLASE /

Chlamydia Trachomatis /

Deubiquitinase.

Function / homology

Function and homology information

deNEDDylase activity / protein deneddylation /

host cell / protein deubiquitination / : / cysteine-type peptidase activity / cysteine-type deubiquitinase activity /

Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / membrane => GO:0016020 /

proteolysis ...
Similarity search - Function

Biological species

Chlamydia trachomatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Ramirez, Y.A. / Kisker, C. / Sauer, F.

Funding support

Germany, 1items

Citation

Journal: Elife / Year: 2017
Title: Chlamydia trachomatis-containing vacuole serves as deubiquitination platform to stabilize Mcl-1 and to interfere with host defense
Authors: Fischer, A. / Harrison, K.S. / Ramirez, Y. / Auer, D. / Chowdhury, S.R. / Prusty, B.K. / Sauer, F. / Dimond, Z. / Kisker, C. / Scott Hefty, P. / Rudel, T.

History

Deposition	May 13, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 29, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed
Revision 1.2	Mar 20, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5b5q.cif.gz	299.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5b5q.ent.gz	247.9 KB	Display	PDB format
PDBx/mmJSON format	5b5q.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/b5/5b5q ftp://data.pdbj.org/pub/pdb/validation_reports/b5/5b5q	HTTPS FTP

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Related structure data

Similar structure data	6fdu-2 6fdq-1 6say-d 2p87-d 6fdu-1 6b00-d 1z97-d 2oki-d 2i82-1 2xms-d Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Membrane thiol protease

B: Membrane thiol protease

hetero molecules

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

1

A: Membrane thiol protease

defined by author&software
27.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Membrane thiol protease

hetero molecules

defined by author&software
28.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	39.100, 77.573, 68.948
Angle α, β, γ (deg.)	90.00, 96.43, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Membrane thiol protease Mass: 27802.246 Da / Num. of mol.: 1 / Fragment: UNP residues 159-401 Source method: isolated from a genetically manipulated source Details: Chlamydia trachomatis deubiquitinase 1 / Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: cdu1, ERS066953_00737 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0E9AT26, UniProt: B0B9A0*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein	Membrane thiol protease Mass: 28500.039 Da / Num. of mol.: 1 / Fragment: UNP residues 155-401 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Gene: CT868 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: K0GC10, UniProt: B0B9A0*PLUS
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 551 / 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: 1.85 Å³/Da / Density % sol: 33.35 % / Description: Plates
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 100mM Bicine pH 9.0, 10% PEG20000, 2% 1,4dioxane, 5% DMSO

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 1.65→77.24 Å / Num. obs: 50612 / % possible obs: 98.1 % / Redundancy: 5.5 % / CC_1/2: 0.993 / R_merge(I) obs: 0.093 / Net I/σ(I): 12.4
Reflection shell	Resolution: 1.65→1.68 Å / % possible all: 98.3

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.7→38.854 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2134	2228	4.96 %
R_work	0.1653	-	-
obs	0.1677	44894	99.79 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.7→38.854 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3898	0	1	551	4450

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4042
X-RAY DIFFRACTION	f_angle_d	0.941	5515
X-RAY DIFFRACTION	f_dihedral_angle_d	11.834	1495
X-RAY DIFFRACTION	f_chiral_restr	0.037	612
X-RAY DIFFRACTION	f_plane_restr	0.004	700

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7001-1.737	0.3281	128	0.2708	2622	X-RAY DIFFRACTION	100
1.737-1.7774	0.3171	145	0.2677	2696	X-RAY DIFFRACTION	100
1.7774-1.8219	0.3001	150	0.2465	2590	X-RAY DIFFRACTION	100
1.8219-1.8711	0.2555	146	0.2299	2692	X-RAY DIFFRACTION	100
1.8711-1.9262	0.233	166	0.2021	2641	X-RAY DIFFRACTION	100
1.9262-1.9884	0.2592	136	0.1937	2633	X-RAY DIFFRACTION	100
1.9884-2.0594	0.2348	147	0.1766	2666	X-RAY DIFFRACTION	100
2.0594-2.1419	0.2051	125	0.1652	2646	X-RAY DIFFRACTION	100
2.1419-2.2394	0.2091	133	0.1603	2690	X-RAY DIFFRACTION	100
2.2394-2.3574	0.2177	124	0.1525	2673	X-RAY DIFFRACTION	100
2.3574-2.5051	0.1959	139	0.1467	2669	X-RAY DIFFRACTION	100
2.5051-2.6984	0.1902	143	0.1484	2660	X-RAY DIFFRACTION	100
2.6984-2.9699	0.1957	147	0.1514	2677	X-RAY DIFFRACTION	100
2.9699-3.3995	0.2019	115	0.1474	2700	X-RAY DIFFRACTION	100
3.3995-4.2821	0.1817	136	0.1285	2694	X-RAY DIFFRACTION	100
4.2821-38.8639	0.1846	148	0.1554	2717	X-RAY DIFFRACTION	99

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	1.7987	-0.6389	0.011	1.0751	0.1969	1.3347	0.1292	0.2155	-0.0309	-0.1461	-0.085	0.0605	-0.2029	-0.1996	-0.0435	0.2129	0.0172	0.0306	0.1112	0.0161	0.0809	29.0667	-7.1328	74.0357
2	3.3302	2.0348	-0.12	8.9606	0.1699	3.8399	-0.0562	-0.0813	0.0952	-0.5392	0.2641	-0.6519	-0.0911	0.2982	-0.1624	0.1547	-0.0101	0.0512	0.1459	-0.0516	0.1775	45.2707	-1.631	82.4448
3	0.842	0.6362	1.4203	2.3043	-0.0413	5.1629	-0.1425	0.1627	0.0879	-0.4492	0.1789	-0.4326	-0.8216	0.6212	-0.0479	0.5018	-0.0802	0.1333	0.2247	0.0036	0.2865	42.4566	6.5197	75.5763
4	0.699	-0.0549	-0.2251	2.4292	1.0904	1.8847	-0.0181	-0.0573	0.0156	-0.0439	0.0983	-0.0655	-0.069	0.0702	-0.0596	0.1381	0.0032	0.0142	0.0776	0.012	0.0637	37.0023	-14.6038	77.4336
5	6.1042	-0.2855	5.1406	1.1704	-0.2163	7.7843	0.0237	0.3547	0.0495	-0.2993	0.1143	-0.0685	0.1476	0.286	-0.0563	0.2334	-0.0045	0.043	0.095	0.0252	0.0929	39.2155	-19.9238	65.544
6	1.3654	0.9472	0.5565	2.0876	0.6238	1.8697	-0.011	-0.0224	0.0804	-0.023	-0.0472	0.1023	-0.0425	-0.0964	0.0781	0.0953	0.0101	0.0207	0.0784	0.0013	0.0782	32.3997	-14.8907	83.7401
7	4.8228	3.4443	0.549	2.6806	1.0985	2.5659	0.1129	-0.2073	-0.2273	0.1629	0.023	-0.364	0.0391	0.1233	-0.1338	0.1108	0.0207	0.0169	0.0936	-0.0135	0.1267	43.2329	-10.9378	92.3913
8	3.3944	1.8635	1.0464	3.4372	0.685	1.9716	0.1706	-0.2667	0.0463	0.2009	-0.1776	0.1684	-0.0156	-0.1979	0.0629	0.183	0.0176	0.074	0.0682	-0.0101	0.096	30.4603	-12.8416	89.899
9	1.0397	0.5019	0.0703	1.9427	0.9832	1.2188	-0.0206	0.0735	0.0587	-0.2154	-0.0826	0.2306	-0.2148	-0.2884	0.0176	0.1726	0.0403	-0.0138	0.1182	-0.0016	0.1042	20.7436	-8.0776	79.4945
10	1.5549	-0.3133	0.394	0.2777	0.0027	0.4517	-0.0014	-0.0662	0.033	-0.0213	-0.0011	0.0228	0.0295	-0.0636	0.0061	0.1642	-0.0105	0.0159	0.0953	0.0046	0.1002	24.7595	30.5789	95.7573
11	1.8215	-1.9711	0.53	2.4392	-0.36	2.1284	-0.0511	0.0516	-0.1882	0.1653	0.1272	-0.6458	0.08	0.1225	-0.0603	0.1486	-0.0039	0.0191	0.1066	-0.0127	0.2374	44.763	22.8916	91.8565
12	3.4223	-1.8291	-1.124	2.9172	0.0754	2.9304	-0.1395	-0.1696	-0.3967	0.4616	0.1051	-0.2245	0.5734	0.2231	0.0395	0.2588	0.0415	-0.0226	0.1169	-0.0015	0.25	39.9353	15.3019	99.0174
13	1.2867	-1.24	-0.7911	3.5988	-0.4026	1.0651	-0.039	-0.0844	0.096	-0.0608	0.1791	-0.3037	-0.3332	0.2699	-0.0818	0.193	-0.0468	0.0274	0.1185	0.0087	0.0793	35.0387	36.5979	95.3484
14	8.9425	0.1675	-4.4454	3.7775	-0.2887	6.9012	-0.1388	-0.442	-0.026	0.4435	0.0827	-0.0552	-0.1522	0.6648	0.0382	0.227	-0.0098	-0.0037	0.1481	0.0089	0.0866	34.269	41.8207	107.3749
15	1.2169	-0.0923	-0.4861	1.7872	-0.7004	1.1932	0.0459	-0.0039	0.0041	-0.0253	-0.0096	-0.0138	-0.0798	0.0442	-0.0291	0.1077	-0.0109	-0.0035	0.0641	-0.0019	0.0577	31.9877	36.3	87.9678
16	4.2966	-3.2002	-0.0451	8.494	0.3361	2.0524	0.1111	0.115	-0.011	-0.1596	-0.0511	-0.1843	-0.1858	0.2459	-0.0444	0.1071	-0.0218	0.0077	0.1028	-0.0062	0.069	44.4993	32.9633	82.0536
17	7.2227	-4.7735	-2.2067	4.9968	1.4026	1.4083	0.094	0.255	-0.1258	-0.0838	-0.1687	0.1016	0.0779	-0.079	0.0911	0.1415	-0.0366	-0.0268	0.0617	-0.0117	0.0547	32.7543	33.465	81.0417
18	2.2026	-1.097	-0.5799	2.9641	0.6635	2.2412	0.085	0.1673	-0.0117	-0.2268	-0.0987	0.1166	0.0647	-0.1401	0.0224	0.1164	-0.0144	0.0138	0.0828	0.0108	0.0816	21.3216	32.1004	83.4192
19	2.6077	-2.3291	1.4413	3.3127	-1.8485	2.1633	-0.19	-0.2606	-0.1762	0.1521	0.2682	0.1908	0.0719	-0.3342	-0.0999	0.1444	-0.0298	0.0276	0.1265	-0.0093	0.1236	17.9722	27.2922	96.5684

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 159 through 198 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 199 through 214 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 215 through 238 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 239 through 254 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 255 through 268 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 269 through 301 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 302 through 321 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 322 through 344 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 345 through 401 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 153 through 198 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 199 through 215 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 216 through 238 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 239 through 254 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 255 through 268 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 269 through 301 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 302 through 321 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 322 through 344 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 345 through 371 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 372 through 401 )

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