PDB-5oed: Human Rab32:GDP in complex with Salmonella GtgE C45A mutant

ID or keywords:

Entry

Database: PDB / ID: 5oed

Title

Human Rab32:GDP in complex with Salmonella GtgE C45A mutant

Components

GtgE
Ras-related protein Rab-32

Keywords

HYDROLASE / Rab GTPase / Posttranslational Modification / Proteolysis / Salmonella Infection

Function / homology

Function and homology information

BLOC-2 complex binding / AP-3 adaptor complex binding / AP-1 adaptor complex binding / endosome to melanosome transport / phagosome maturation / melanosome assembly / mitochondria-associated endoplasmic reticulum membrane contact site / GTP-dependent protein binding / RAB geranylgeranylation / melanosome membrane ...
Similarity search - Function

Biological species

Salmonella choleraesuis (bacteria)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Wachtel, R. / Braeuning, B. / Mader, S.L. / Ecker, F. / Kaila, V.R.I. / Groll, M. / Itzen, A.

Funding support

Germany, 1items

Citation

Journal: Nat Commun / Year: 2018
Title: The protease GtgE from Salmonella exclusively targets inactive Rab GTPases.
Authors: Wachtel, R. / Brauning, B. / Mader, S.L. / Ecker, F. / Kaila, V.R.I. / Groll, M. / Itzen, A.

History

Deposition	Jul 7, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 10, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2018	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Jan 17, 2024	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 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5oed.cif.gz	230.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5oed_validation.pdf.gz	746.9 KB	Display	wwPDB validaton report
Full document	5oed_full_validation.pdf.gz	747.9 KB	Display
Data in XML	5oed_validation.xml.gz	14.9 KB	Display
Data in CIF	5oed_validation.cif.gz	19.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oe/5oed ftp://data.pdbj.org/pub/pdb/validation_reports/oe/5oed	HTTPS FTP

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Related structure data

Related structure data	5oecSC 4cym 4mi7 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5es1-d 1sg6-2 2wjw-d 6ff8-d 4loj-d 6ija-1 6ws0-d 6s26-d 6a03-d 4qta-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

Deposited unit

A: GtgE

B: Ras-related protein Rab-32

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	67.410, 67.410, 427.340
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	GtgE / Virulence protein Mass: 26357.350 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella choleraesuis (bacteria) / Gene: gtgE, IN36_21720, IN69_16745, IN77_18825 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6EAT3
#2: Protein	Ras-related protein Rab-32 Mass: 20901.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13637
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.96 Å³/Da / Density % sol: 58.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 50 mM Imidazole, 20% PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 13, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.9→50 Å / Num. obs: 13564 / % possible obs: 96.8 % / Redundancy: 5.1 % / R_merge(I) obs: 0.062 / Net I/σ(I): 18.9
Reflection shell	Resolution: 2.9→3 Å / R_merge(I) obs: 0.532 / Mean I/σ(I) obs: 2.9 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5OEC

5oec

Resolution: 2.9→14.997 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.76

	R_factor	Num. reflection	% reflection
R_free	0.2404	1343	9.97 %
R_work	0.2009	-	-
obs	0.2047	13425	97.73 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.9→14.997 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2906	0	29	13	2948

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3003
X-RAY DIFFRACTION	f_angle_d	0.527	4066
X-RAY DIFFRACTION	f_dihedral_angle_d	15.933	1773
X-RAY DIFFRACTION	f_chiral_restr	0.038	448
X-RAY DIFFRACTION	f_plane_restr	0.002	517

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 (%)
2.9-2.9588	0.345	144	0.3427	1255	X-RAY DIFFRACTION	99
2.9588-3.0226	0.3487	139	0.3037	1240	X-RAY DIFFRACTION	99
3.0226-3.0923	0.3096	145	0.2691	1261	X-RAY DIFFRACTION	99
3.0923-3.169	0.2876	136	0.2683	1235	X-RAY DIFFRACTION	98
3.169-3.2538	0.2984	141	0.2857	1255	X-RAY DIFFRACTION	99
3.2538-3.3485	0.3119	136	0.2642	1259	X-RAY DIFFRACTION	99
3.3485-3.4553	0.278	134	0.2265	1217	X-RAY DIFFRACTION	97
3.4553-3.5772	0.2201	131	0.2237	1213	X-RAY DIFFRACTION	94
3.5772-3.7184	0.2441	139	0.2139	1249	X-RAY DIFFRACTION	99
3.7184-3.8848	0.266	133	0.2075	1236	X-RAY DIFFRACTION	99
3.8848-4.0857	0.2429	141	0.1973	1233	X-RAY DIFFRACTION	98
4.0857-4.3358	0.1932	132	0.1682	1263	X-RAY DIFFRACTION	98
4.3358-4.6613	0.1806	136	0.1533	1189	X-RAY DIFFRACTION	94
4.6613-5.1134	0.2119	137	0.1554	1249	X-RAY DIFFRACTION	98
5.1134-5.8152	0.2275	142	0.1835	1243	X-RAY DIFFRACTION	99
5.8152-7.1896	0.2571	133	0.2137	1216	X-RAY DIFFRACTION	96
7.1896-14.9968	0.2247	131	0.1667	1232	X-RAY DIFFRACTION	96

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	4.3505	0.1213	2.3176	1.4156	1.0899	5.0591	-0.1077	-0.6161	-0.1802	0.2774	-0.2174	0.202	0.8928	-1.2105	-0.1332	0.5096	-0.0437	0.0195	0.8871	-0.1529	0.6972	14.6629	-31.0671	20.2162
2	3.1383	2.4949	2.4804	5.9348	2.5985	2.049	0.6917	-0.7904	0.4092	1.2616	-0.6053	-0.1966	0.4688	-0.997	-0.4673	0.6209	-0.1595	0.1189	1.3573	-0.1237	0.7558	9.5922	-29.7763	30.2589
3	3.2596	1.4895	2.8418	4.5981	-0.4674	3.2654	0.2347	0.6713	0.3738	0.1579	0.3236	1.0112	-0.8028	-1.4503	0.13	0.6218	-0.0058	0.0701	1.2147	-0.0987	1.0265	3.7149	-21.3803	16.114
4	3.3885	0.0029	1.2476	3.5041	0.2855	4.6072	-0.1865	-0.246	0.8674	0.3009	0.0636	0.0835	-0.5942	0.2111	-0.023	0.5417	0.1305	0.0052	0.8621	-0.2142	0.5504	26.2263	-15.2509	24.2305
5	2.7239	-0.281	1.3218	1.3271	-0.0687	3.1697	0.1809	0.5677	-0.3651	0.0554	0.028	-0.247	0.5854	0.4554	0.0347	0.3687	0.1362	-0.0567	0.7897	-0.235	0.7132	28.9433	-26.2896	19.8734
6	5.1246	3.7694	-0.2775	3.3897	-2.2018	6.5898	0.5199	1.421	2.3836	-0.0935	0.0701	0.4055	-2.4729	0.3162	0.3791	0.9105	-0.0307	-0.1822	1.2335	0.1382	1.0472	24.3752	-9.9846	14.013
7	4.8365	1.2158	2.7457	4.5391	0.7056	5.694	-0.1584	-0.5964	-0.2387	1.0859	0.2211	-0.5747	0.5493	-1.0516	-0.1581	0.5393	0.1497	-0.0553	0.9583	-0.2799	0.7452	25.3453	-24.9566	35.9028
8	3.0585	0.559	-0.6853	2.5194	1.4026	2.2326	-0.1507	0.1014	-0.0531	-0.3088	0.3558	0.5296	-0.2348	0.3434	-0.0811	0.3323	-0.0125	-0.0229	1.1263	-0.1457	0.6388	15.6594	-24.8774	-2.3982
9	3.3061	-1.3576	-1.5905	1.0792	-0.412	3.2826	0.6287	0.833	0.0702	-0.7145	-0.3121	0.439	-1.1693	-0.0336	-0.3059	0.8146	0.1671	0.0474	1.4416	-0.1659	1.0151	7.1132	-13.1073	4.1837
10	2.0037	-0.0403	-0.7728	2.6595	-1.2756	1.2962	-0.2628	0.2664	-0.386	-0.6594	0.1277	0.7293	0.2589	0.0326	0.066	0.2964	0.0857	-0.041	0.9143	-0.1575	0.7259	12.9545	-32.2059	0.4528
11	3.2371	0.7795	-3.9492	1.5752	-3.4085	9.19	0.6308	-0.1078	0.7326	0.6666	0.482	-0.3534	-0.9663	0.1849	0.1384	0.5404	-0.2071	-0.0027	1.2325	-0.2988	0.9635	27.9684	-15.2282	1.8965
12	4.4836	0.4862	-1.3806	1.8387	1.6824	2.2987	0.0341	-0.1254	-0.6231	0.0646	0.7055	-0.1853	-0.2839	0.9301	0.0928	0.3257	-0.0147	0.1264	1.1692	-0.1164	0.5574	25.2261	-24.2644	-2.3014
13	3.4752	-0.8527	-2.0912	1.9469	0.6911	3.2276	-0.3891	0.9783	0.7184	-1.1067	0.9557	1.0001	-1.5047	0.4251	-0.5656	1.2921	-0.1742	0.2289	1.2601	0.114	1.0836	23.4792	-9.3035	-13.8308
14	2.3195	-1.583	0.2449	4.5105	2.4612	2.0598	-0.2535	-0.6812	-0.459	-0.8039	0.82	-0.2601	-0.3348	0.4148	0.1113	0.5268	-0.0757	-0.0023	1.6021	-0.2428	0.7633	31.7351	-26.0649	-7.478
15	4.104	-0.7657	-0.6603	3.2891	0.9485	1.5864	0.5725	0.7899	0.1002	0.1223	0.5699	-0.255	-0.2266	0.2067	0.6385	0.4922	0.0818	0.0252	1.3018	-0.0021	0.3189	18.8121	-18.5392	-17.5288
16	2.4078	-1.0159	-0.5703	2.6001	0.8244	3.8177	0.4149	0.9547	0.3645	-0.3761	-0.2568	0.1861	-0.7465	-0.5648	-0.1787	0.646	-0.028	0.0603	1.3159	0.0646	0.9193	17.6801	-20.6146	-16.2504
17	2.683	-1.1033	-0.0268	0.6314	-0.3251	0.8422	0.0071	0.6929	-0.8157	-0.3335	0.342	0.0345	0.0899	-0.5119	1.5495	0.3231	-0.1716	0.0362	1.4476	-0.3771	0.8359	15.8015	-32.05	-11.2977

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 54 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 82 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 83 through 117 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 118 through 191 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 192 through 203 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 204 through 217 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 21 through 47 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 48 through 57 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 58 through 81 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 82 through 92 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 93 through 107 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 108 through 116 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 117 through 136 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 137 through 160 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 161 through 180 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 181 through 195 )

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