PDB-5uf8: Crystal structure of the ARF family small GTPase ARF2 from Candid...

ID or keywords:

Entry

Database: PDB / ID: 5uf8

Title

Crystal structure of the ARF family small GTPase ARF2 from Candida albicans in complex with GDP

Components

Potential ADP-ribosylation factor

Keywords

SIGNALING PROTEIN /

Signalling protein /

GTPase / GDP / GTP / ARF family /

structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID /

National Institute of Allergy and Infectious Diseases

Function / homology

Function and homology information

cellular response to xenobiotic stimulus => GO:0071466 / filamentous growth / vesicle-mediated transport /

intracellular protein transport /

GTPase activity / GTP binding /

plasma membrane
Similarity search - Function

Biological species

Candida albicans (yeast)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.872 Å

Authors

Stogios, P.J. / Skarina, T. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of the ARF family small GTPase ARF2 from Candida albicans in complex with GDP
Authors: Stogios, P.J.

History

Deposition	Jan 3, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 25, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5uf8.cif.gz	284.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5uf8.ent.gz	232.3 KB	Display	PDB format
PDBx/mmJSON format	5uf8.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/uf/5uf8 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/5uf8	HTTPS FTP

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Related structure data

Related structure data	1mr3S S: Starting model for refinement
Similar structure data	5xcj-1 3k9n-d 1ciz-d 1gnp-d 4pv6-6 1n08-2 6mnx-4 1xnb-d 1n07-2 2z79-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Other databases	TargetTrack: IDP95558

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Potential ADP-ribosylation factor

B: Potential ADP-ribosylation factor

C: Potential ADP-ribosylation factor

D: Potential ADP-ribosylation factor

hetero molecules

84.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Potential ADP-ribosylation factor

hetero molecules

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

2

B: Potential ADP-ribosylation factor

hetero molecules

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

3

C: Potential ADP-ribosylation factor

hetero molecules

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

4

D: Potential ADP-ribosylation factor

hetero molecules

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

Unit cell

Length a, b, c (Å)	38.289, 64.362, 79.236
Angle α, β, γ (deg.)	78.11, 83.73, 72.77
Int Tables number	1
Space group name H-M	P1

#1: Protein	Potential ADP-ribosylation factor Mass: 20593.467 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / Gene: ARF2, orf19.5964, CaO19.13385, CaO19.5964 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: Q5AND9
#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 531 / 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: 2.21 Å³/Da / Density % sol: 44.41 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30% PEG2K MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 5 mM magnesium chloride, 5 mM ADP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 13, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.88→25 Å / Num. obs: 53906 / % possible obs: 93.4 % / Redundancy: 4.1 % / R_merge(I) obs: 0.054 / Net I/σ(I): 41.35
Reflection shell	Resolution: 1.88→1.91 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.409 / Mean I/σ(I) obs: 5.04 / CC_1/2: 0.838 / % possible all: 90.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2481: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
BALBES		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1MR3

1mr3

Resolution: 1.872→24.873 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 29.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2698	1950	3.72 %	RANDOM SELECTION
R_work	0.235	-	-	-
obs	0.2364	52456	90.14 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.872→24.873 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5154	0	112	531	5797

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5373
X-RAY DIFFRACTION	f_angle_d	0.647	7313
X-RAY DIFFRACTION	f_dihedral_angle_d	19.394	1985
X-RAY DIFFRACTION	f_chiral_restr	0.046	829
X-RAY DIFFRACTION	f_plane_restr	0.003	916

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 (%)
1.8715-1.9183	0.2614	111	0.255	2930	X-RAY DIFFRACTION	74
1.9183-1.9702	0.3265	134	0.2687	3382	X-RAY DIFFRACTION	85
1.9702-2.0281	0.3168	138	0.2558	3520	X-RAY DIFFRACTION	87
2.0281-2.0935	0.3344	132	0.2558	3477	X-RAY DIFFRACTION	88
2.0935-2.1683	0.3019	137	0.2626	3590	X-RAY DIFFRACTION	89
2.1683-2.2551	0.2987	140	0.2515	3605	X-RAY DIFFRACTION	90
2.2551-2.3576	0.3126	139	0.2658	3594	X-RAY DIFFRACTION	90
2.3576-2.4818	0.3101	142	0.2506	3679	X-RAY DIFFRACTION	91
2.4818-2.6372	0.2966	141	0.2527	3666	X-RAY DIFFRACTION	92
2.6372-2.8405	0.2846	145	0.2568	3698	X-RAY DIFFRACTION	93
2.8405-3.1259	0.3201	146	0.2539	3789	X-RAY DIFFRACTION	94
3.1259-3.577	0.2429	147	0.2225	3817	X-RAY DIFFRACTION	95
3.577-4.5023	0.2108	148	0.2046	3843	X-RAY DIFFRACTION	96
4.5023-24.875	0.2543	150	0.2178	3916	X-RAY DIFFRACTION	98

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	9.7282	-0.2616	4.7295	7.074	-1.7176	2.6579	0.4849	-0.2799	-0.8234	0.4232	0.3964	-0.8875	0.9519	-0.0227	-0.7779	0.3059	0.0229	-0.0557	0.3652	-0.0121	0.4398	7.3037	-1.1448	9.9736
2	1.4252	0.2792	0.1641	3.6482	0.6773	3.4756	0.0361	-0.0438	0.1873	0.056	0.004	0.0374	0.0945	-0.0297	-0.0498	0.1857	-0.0284	-0.0032	0.2539	-0.0086	0.2572	4.3187	8.6463	4.6644
3	6.4829	1.3865	-6.7201	2.1246	-1.6282	7.0148	-0.0691	1.8411	-0.6238	-0.5771	-0.395	0.6669	-0.402	-0.6649	0.4131	0.4787	-0.0419	-0.0145	0.6919	-0.1752	0.6719	15.0104	5.0695	-7.9592
4	3.1428	0.0306	-1.0792	7.1899	-3.8356	3.16	-0.4689	-0.4517	-0.2034	0.6666	0.5035	-0.8524	-0.2382	-0.2273	-0.0228	0.4141	-0.1608	-0.102	0.592	-0.051	0.4028	15.9197	-0.422	2.469
5	3.3423	-0.5584	0.6487	3.9002	-0.9922	2.8831	0.01	0.2785	-0.0981	-0.3516	-0.0349	-0.1662	0.308	-0.0412	0.016	0.2507	-0.0412	0.0227	0.2567	-0.0105	0.2576	-1.0855	-3.0739	-6.7857
6	2.0043	-0.4879	-0.3186	5.2082	-0.5477	4.3369	0.0142	-0.1196	-0.0118	0.1772	-0.0371	0.0186	0.478	-0.2125	-0.0216	0.2539	-0.0575	0.0293	0.2535	0.0314	0.2894	-6.8374	-4.0033	4.2265
7	5.9269	0.7286	1.7403	2.559	-1.673	6.9727	-0.2622	-0.4924	0.1304	0.3937	0.0932	0.153	-0.8117	-0.1862	0.1638	0.2723	-0.0011	-0.0065	0.1847	0.0165	0.293	-11.144	-34.6971	1.277
8	2.3038	1.9788	0.799	2.7184	-0.7906	2.0364	-0.0156	-0.002	0.3253	0.1394	0.0218	0.0424	-0.2638	-0.091	-0.0433	0.3568	0.0237	0.0058	0.2535	-0.0407	0.255	-16.2684	-40.4691	5.7033
9	7.1596	1.0796	0.8274	8.3542	4.505	3.1403	-0.7634	0.1176	0.1349	0.5033	0.1115	0.6231	-0.1945	1.0552	0.5547	0.3163	-0.0907	0.0408	0.2281	0.0361	0.3256	-15.8082	-33.7178	3.799
10	3.4907	-3.505	0.1339	8.9011	-6.6931	8.0933	-0.32	-0.6645	-0.0336	1.456	1.3076	0.478	-0.8656	-2.3196	-0.6113	0.4456	0.1146	0.0757	0.8016	0.0167	0.614	-25.4618	-29.8554	4.1411
11	3.7126	0.7438	-1.1625	3.3289	-0.3206	8.0543	-0.0229	0.2696	0.1998	-0.1931	0.0964	0.2163	0.3134	-0.2421	-0.0662	0.2755	-0.0238	-0.0008	0.1864	0.0242	0.3375	-14.1853	-29.6924	-10.4382
12	2.7168	-0.2781	0.7867	5.9863	-0.7697	5.6541	-0.1385	-0.0478	0.1463	0.1213	-0.0514	-0.0643	-0.5243	0.0202	0.1897	0.2052	-0.0681	-0.0048	0.2046	0.0019	0.272	-7.789	-24.5746	-5.5957
13	6.7475	4.9396	-4.812	6.9221	-5.0309	4.1957	0.0118	0.4263	0.1024	-0.5709	-0.3906	-0.1806	0.277	0.6564	0.4556	0.3115	0.1458	0.0192	0.4544	0.0876	0.3227	14.6288	18.2104	31.6097
14	4.6703	-0.9534	0.7971	3.4806	1.0478	2.9916	0.0661	0.3247	-0.0114	-0.1439	0.0225	-0.2275	-0.3169	0.0901	-0.078	0.2158	0.0199	0.0027	0.2091	0.024	0.244	13.0748	9.8438	33.7069
15	5.1919	3.9965	-2.5878	4.2179	-1.3203	2.3522	0.2332	-0.4424	0.1123	-0.0096	-0.9487	-0.3237	-0.5111	0.3951	0.711	0.3931	0.1951	0.0117	0.6233	-0.0859	0.5663	24.9801	15.1496	42.1317
16	4.6367	0.3937	-2.877	3.1536	-3.2218	8.7092	0.0151	-0.5156	0.3658	0.0921	-0.2785	-0.4425	-0.3295	0.7505	0.2581	0.2363	0.0372	-0.0289	0.2512	-0.0061	0.331	12.6297	20.4137	44.2744
17	6.3224	1.5821	0.1993	6.3449	0.3345	1.5354	0.1467	-0.2476	0.5177	0.818	-0.1152	0.2039	-0.2571	-0.238	-0.0026	0.3188	0.088	-0.0283	0.3243	0.0359	0.2324	2.4634	20.8983	43.9557
18	2.6879	0.5228	-0.88	4.7261	0.1165	2.0536	-0.0072	0.1505	0.2494	0.0003	0.1205	0.0937	-0.382	-0.309	-0.1015	0.2572	0.0636	-0.0098	0.2737	0.0273	0.2348	2.8999	24.4906	36.922
19	8.7572	-3.1843	-0.2683	2.8658	-3.9451	9.4971	0.3049	1.1003	-1.7206	-2.9871	-0.6088	1.1696	0.9136	-0.1326	0.3569	1.1651	-0.059	-0.2459	0.4913	-0.1031	0.877	31.0635	44.4457	23.5721
20	3.009	0.0433	2.0894	3.8252	-2.439	3.3485	-0.0226	0.1983	-0.1602	-0.1915	-0.0227	-0.0886	0.1052	0.0695	0.0424	0.2069	0.0337	0.012	0.281	-0.0298	0.2697	33.4029	55.9188	34.1086
21	4.1423	-1.4351	2.2281	2.438	-1.585	1.5355	-0.1634	0.9191	-0.4728	-0.4679	-0.3422	1.718	0.2287	-1.0578	0.2277	0.327	-0.0195	-0.087	0.8929	-0.1969	0.8251	22.4682	48.5428	34.8947
22	3.485	0.3626	0.3436	2.0364	0.8222	8.545	0.0254	-0.3792	-0.1853	0.1355	0.0626	0.005	-0.3789	0.0652	-0.1036	0.2887	0.0376	0.005	0.1935	-0.0127	0.4044	32.8149	48.8602	50.122
23	1.7688	-1.0928	0.3444	4.7916	0.0109	7.1785	-0.0797	-0.1525	-0.0783	0.1607	-0.047	0.343	-0.0024	-0.5476	0.1142	0.2215	0.0542	0.0103	0.195	0.0046	0.3642	36.524	44.6555	46.7425
24	2.1056	-0.1234	-1.4636	4.3193	-0.3545	4.896	-0.2144	0.3258	-0.0176	-0.2238	0.0328	-0.0051	0.4227	-0.0615	0.1909	0.2427	0.0578	0.0193	0.2562	-0.0011	0.3834	41.5795	41.7709	40.438

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 17:21 )	A	17 - 21
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 22:68 )	A	22 - 68
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 69:77 )	A	69 - 77
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 78:84 )	A	78 - 84
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 85:149 )	A	85 - 149
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 150:177 )	A	150 - 177
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 17:36 )	B	17 - 36
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 37:56 )	B	37 - 56
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 57:72 )	B	57 - 72
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 75:84 )	B	75 - 84
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 85:109 )	B	85 - 109
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 110:177 )	B	110 - 177
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 17:24 )	C	17 - 24
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 25:70 )	C	25 - 70
15	X-RAY DIFFRACTION	15	( CHAIN C AND RESID 71:81 )	C	71 - 81
16	X-RAY DIFFRACTION	16	( CHAIN C AND RESID 82:115 )	C	82 - 115
17	X-RAY DIFFRACTION	17	( CHAIN C AND RESID 116:141 )	C	116 - 141
18	X-RAY DIFFRACTION	18	( CHAIN C AND RESID 142:177 )	C	142 - 177
19	X-RAY DIFFRACTION	19	( CHAIN D AND RESID 14:19 )	D	14 - 19
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 20:67 )	D	20 - 67
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 68:86 )	D	68 - 86
22	X-RAY DIFFRACTION	22	( CHAIN D AND RESID 87:109 )	D	87 - 109
23	X-RAY DIFFRACTION	23	( CHAIN D AND RESID 110:143 )	D	110 - 143
24	X-RAY DIFFRACTION	24	( CHAIN D AND RESID 144:177 )	D	144 - 177

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