PDB-5oec: Human Rab32 (18-201):GDP in complex with Salmonella GtgE (21-214)...

ID or keywords:

Entry

Database: PDB / ID: 5oec

Title

Human Rab32 (18-201):GDP in complex with Salmonella GtgE (21-214) 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 / melanosome assembly / phagosome maturation / 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: 2.3 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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	5oec.cif.gz	164.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5oec.ent.gz	130.2 KB	Display	PDB format
PDBx/mmJSON format	5oec.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oe/5oec ftp://data.pdbj.org/pub/pdb/validation_reports/oe/5oec	HTTPS FTP

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Related structure data

Related structure data	5oedC 4cymS 4mi7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5qcr-3 5qcr-1 6nv7-3 4lxk-3 4dus-d 3k17-3 3rtn-d 6uj0-2 2f3f-3 4lxm-1 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	#148 - Apr 2012 Ras Protein similarity (1) #245 - May 2020 Spliceosomes similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: GtgE

B: Ras-related protein Rab-32

hetero molecules

44 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)	47.822, 66.993, 110.987
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	GtgE / Virulence protein Mass: 22601.102 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: 20941.842 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-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
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.04 Å³/Da / Density % sol: 39.77 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 100 mM Bis-Tris, 25% PEG 3350

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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: 2.3→50 Å / Num. obs: 16142 / % possible obs: 97.4 % / Redundancy: 5.1 % / R_merge(I) obs: 0.082 / Net I/σ(I): 13.8
Reflection shell	Resolution: 2.3→2.4 Å / R_merge(I) obs: 0.523 / Mean I/σ(I) obs: 3.6 / % possible all: 93

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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: 4CYM, 4MI7

4cym

4mi7

Resolution: 2.3→14.954 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.86

	R_factor	Num. reflection	% reflection
R_free	0.2452	1603	9.94 %
R_work	0.2077	-	-
obs	0.2116	16068	96.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→14.954 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2838	0	29	55	2922

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	2932
X-RAY DIFFRACTION	f_angle_d	0.435	3970
X-RAY DIFFRACTION	f_dihedral_angle_d	16.128	1732
X-RAY DIFFRACTION	f_chiral_restr	0.038	436
X-RAY DIFFRACTION	f_plane_restr	0.003	506

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 (%)
2.2941-2.3315	0.3332	116	0.3082	1096	X-RAY DIFFRACTION	84
2.3315-2.3716	0.3767	135	0.3041	1216	X-RAY DIFFRACTION	92
2.3716-2.4145	0.3186	144	0.2816	1306	X-RAY DIFFRACTION	98
2.4145-2.4608	0.3547	146	0.2662	1254	X-RAY DIFFRACTION	99
2.4608-2.5108	0.3144	149	0.2609	1331	X-RAY DIFFRACTION	98
2.5108-2.5651	0.332	136	0.2597	1270	X-RAY DIFFRACTION	98
2.5651-2.6245	0.276	142	0.2396	1284	X-RAY DIFFRACTION	99
2.6245-2.6897	0.3278	143	0.2413	1324	X-RAY DIFFRACTION	98
2.6897-2.762	0.2663	149	0.2328	1303	X-RAY DIFFRACTION	99
2.762-2.8428	0.3053	141	0.2324	1272	X-RAY DIFFRACTION	97
2.8428-2.9338	0.2884	139	0.2328	1240	X-RAY DIFFRACTION	94
2.9338-3.0379	0.2878	147	0.2372	1298	X-RAY DIFFRACTION	99
3.0379-3.1584	0.2599	145	0.2286	1334	X-RAY DIFFRACTION	99
3.1584-3.3007	0.246	138	0.2195	1281	X-RAY DIFFRACTION	99
3.3007-3.4726	0.2784	145	0.2159	1294	X-RAY DIFFRACTION	99
3.4726-3.6872	0.2258	147	0.1962	1307	X-RAY DIFFRACTION	98
3.6872-3.9669	0.218	135	0.1834	1256	X-RAY DIFFRACTION	95
3.9669-4.3571	0.2131	146	0.1621	1303	X-RAY DIFFRACTION	99
4.3571-4.9673	0.1624	140	0.1567	1287	X-RAY DIFFRACTION	98
4.9673-6.1837	0.2208	140	0.1926	1286	X-RAY DIFFRACTION	97
6.1837-14.9538	0.1951	137	0.1861	1277	X-RAY DIFFRACTION	97

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	1.077	0.3811	0.4038	1.4288	0.8723	1.905	-0.1795	0.5761	0.0194	-0.5279	0.3066	-0.0557	-0.1921	0.4488	-0.0004	0.5615	-0.0979	-0.016	0.3818	0.009	0.2071	16.3075	26.0165	120.2132
2	2.122	0.8986	1.7496	1.2306	0.488	3.0012	-0.1752	0.2804	0.2303	-0.64	0.2136	0.0057	-0.9634	0.0609	0.3285	1.2584	-0.201	-0.1126	0.7486	0.0259	0.363	10.5408	31.3498	112.2962
3	5.7671	1.4575	-1.1616	2.6883	1.1316	2.0358	-0.2804	0.3119	0.8688	-0.223	0.1163	0.5692	-1.0053	-0.3151	0.2855	0.6703	0.0858	-0.1362	0.3463	0.0029	0.4588	9.5364	37.0797	128.7598
4	2.3896	0.618	1.0717	2.9252	1.0111	1.9182	0.0382	-0.1586	-0.0849	-0.1615	-0.0047	0.6156	0.1095	-0.4874	-0.0762	0.37	-0.0089	-0.1263	0.3344	0.0312	0.374	0.2809	14.6506	124.1702
5	1.8573	0.8027	0.7125	2.7691	0.1751	1.9933	0.0285	0.3285	-0.708	-0.2339	0.3421	-0.2281	0.4075	0.1177	-0.2268	0.444	-0.01	-0.0375	0.325	-0.0763	0.3764	12.2772	11.8825	122.6601
6	0.9729	1.2752	0.5058	2.4534	-0.8416	3.1594	0.2073	-0.8374	0.2966	1.21	0.0174	0.9063	-0.1078	-0.7599	-0.0857	0.6116	-0.0245	0.1115	0.6446	0.0967	0.607	0.7954	16.737	135.5528
7	2.2641	-0.435	0.4162	0.3754	-0.3433	1.7038	-0.08	0.7176	-0.0009	-0.5257	-0.0161	0.2242	-0.2618	0.1111	-0.0342	0.601	-0.1204	-0.2703	0.4755	0.0102	0.3955	2.7685	18.2594	112.9408
8	2.2552	0.1823	0.8868	3.0368	1.2202	2.7575	0.5561	-0.3359	-0.3709	0.7068	-0.005	-0.326	0.2359	-0.1266	0.3934	0.5628	-0.0372	-0.1175	0.3117	-0.0536	0.2581	21.0325	24.9475	143.1321
9	0.8485	0.6508	1.3232	2.1694	1.6722	3.2798	-0.0226	-0.9869	0.5852	0.7868	-0.4477	0.6432	-0.0622	-0.8522	0.2649	0.9682	0.0505	0.1897	0.6843	-0.2114	0.5804	8.7527	32.387	144.065
10	4.4654	2.0108	1.747	3.7408	1.271	2.3864	0.1532	0.2695	-0.0835	0.3314	0.2448	-0.4765	0.0723	0.2933	-0.218	0.317	0.0757	-0.0609	0.2495	-0.1164	0.3132	26.7516	27.7211	137.0683
11	3.6	-0.4718	1.3139	4.6462	1.5383	1.195	0.4803	-0.4216	-0.856	1.1158	-0.079	-0.1221	0.5831	-0.2798	-0.2891	0.7616	-0.0053	-0.2354	0.3581	0.0974	0.53	15.3427	12.1246	139.9781
12	4.3209	0.8602	1.7105	0.6567	0.1159	0.7814	0.3724	-1.1761	-0.0755	0.9565	-0.2521	-0.135	-0.1991	-0.3582	-0.0694	1.1471	-0.0485	-0.2387	0.5133	0.0268	0.3916	18.4905	19.8267	152.9076
13	1.33	-0.9464	0.4531	1.6092	-0.5069	0.1908	0.0843	-0.5091	-0.3576	0.8044	0.1494	-0.0013	-0.1914	-0.1339	-0.3719	1.3787	-0.157	-0.4516	0.6163	0.3071	0.7869	18.0364	10.3655	152.4425
14	1.1751	1.2328	0.5355	1.5547	-0.2145	2.5816	0.7133	-0.0532	-0.5919	-0.0889	-0.0864	-0.3941	0.2863	-0.0699	-0.54	1.0417	-0.0742	-0.3945	0.3419	0.0715	0.5525	28.5484	13.983	147.1186
15	2.1198	1.8274	0.1024	1.761	0.7784	2.5594	1.1316	-0.577	-0.9455	0.2289	-0.8245	-0.2531	0.7864	-0.2916	-0.6675	1.6582	-0.2376	-0.4356	0.6546	0.0277	0.7608	22.8889	19.1699	159.17
16	0.9757	0.265	0.6646	0.912	1.2917	2.4385	0.1229	-0.1463	-0.1965	0.6077	-0.0428	-0.2482	0.3734	-0.1524	0.042	1.0886	-0.1292	-0.3668	0.3764	-0.027	0.4393	27.6908	26.7343	151.3695

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 213 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 22 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 98 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 99 through 110 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 111 through 127 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 128 through 143 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 144 through 168 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 169 through 195 )

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