PDB-6ejh: Crystal structure of the G343C mutant of Candida albicans Mep2

ID or keywords:

Entry

Database: PDB / ID: 6ejh

Title

Crystal structure of the G343C mutant of Candida albicans Mep2

Components

Ammonium transporter

Keywords

MEMBRANE PROTEIN / ammonium transporter / Candida albicans / signalling mutant

Function / homology

Function and homology information

filamentous growth of a population of unicellular organisms in response to starvation / ammonium transmembrane transport / ammonium channel activity / filamentous growth / cellular response to nitrogen starvation / cellular response to starvation / plasma membrane
Similarity search - Function

Biological species

Candida albicans (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.71 Å

Authors

van den Berg, B. / van den Berg, B.

Citation

Journal: To Be Published
Title: Crystal structure of the G343C mutant of Candida albicans Mep2
Authors: van den Berg, B.

History

Deposition	Sep 21, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 10, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ejh.cif.gz	191.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6ejh.ent.gz	153.6 KB	Display	PDB format
PDBx/mmJSON format	6ejh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6ejh_validation.pdf.gz	426 KB	Display	wwPDB validaton report
Full document	6ejh_full_validation.pdf.gz	429.3 KB	Display
Data in XML	6ejh_validation.xml.gz	19.1 KB	Display
Data in CIF	6ejh_validation.cif.gz	27.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ej/6ejh ftp://data.pdbj.org/pub/pdb/validation_reports/ej/6ejh	HTTPS FTP

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Related structure data

Related structure data	5af1S 6ej6 S: Starting model for refinement
Similar structure data	5af1-2 5aez-1 6ej6-1 5af1-1 5aex-1 5aex-2 5n4l-2 5n0k-d 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: Ammonium transporter

52.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ammonium transporter

defined by software
Evidence: gel filtration
159 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	104.700, 104.700, 160.210
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	A-605- HOH
2	1	A-694- HOH

#1: Protein	Ammonium transporter Mass: 52835.520 Da / Num. of mol.: 1 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: MEP2, orf19.5672, CAALFM_C400430WA / Production host: Saccharomyces cerevisiae S288c (yeast) / References: UniProt: Q59UP8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.2 Å³/Da / Density % sol: 61.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50 mM Tris pH 8 28% PEG 400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.71→53.4 Å / Num. obs: 70763 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC_1/2: 0.993 / R_pim(I) all: 0.041 / Net I/σ(I): 11.9
Reflection shell	Resolution: 1.71→1.75 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5289 / CC_1/2: 0.691 / R_pim(I) all: 0.34 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
xia2		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5AF1

5af1

Resolution: 1.71→53.4 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 17.51

	R_factor	Num. reflection	% reflection
R_free	0.1909	3666	5.18 %
R_work	0.1714	-	-
obs	0.1725	70757	99.92 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.71→53.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3486	0	0	196	3682

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	3660
X-RAY DIFFRACTION	f_angle_d	1.113	5012
X-RAY DIFFRACTION	f_dihedral_angle_d	2.755	2756
X-RAY DIFFRACTION	f_chiral_restr	0.075	551
X-RAY DIFFRACTION	f_plane_restr	0.008	621

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 (%)
1.71-1.7325	0.2567	160	0.2319	2580	X-RAY DIFFRACTION	100
1.7325-1.7562	0.2678	150	0.217	2585	X-RAY DIFFRACTION	100
1.7562-1.7813	0.221	129	0.2049	2582	X-RAY DIFFRACTION	100
1.7813-1.8079	0.2154	130	0.1867	2590	X-RAY DIFFRACTION	100
1.8079-1.8362	0.1808	120	0.1775	2600	X-RAY DIFFRACTION	100
1.8362-1.8663	0.2128	145	0.1734	2597	X-RAY DIFFRACTION	100
1.8663-1.8985	0.2174	138	0.1698	2547	X-RAY DIFFRACTION	100
1.8985-1.933	0.1877	130	0.1717	2589	X-RAY DIFFRACTION	100
1.933-1.9702	0.1933	155	0.1625	2593	X-RAY DIFFRACTION	100
1.9702-2.0104	0.1919	171	0.1628	2540	X-RAY DIFFRACTION	100
2.0104-2.0541	0.1771	143	0.1615	2573	X-RAY DIFFRACTION	100
2.0541-2.1019	0.1976	118	0.159	2604	X-RAY DIFFRACTION	100
2.1019-2.1544	0.1843	167	0.1559	2545	X-RAY DIFFRACTION	100
2.1544-2.2127	0.1781	160	0.15	2548	X-RAY DIFFRACTION	100
2.2127-2.2778	0.1812	126	0.1525	2630	X-RAY DIFFRACTION	100
2.2778-2.3513	0.1937	135	0.1551	2562	X-RAY DIFFRACTION	100
2.3513-2.4354	0.1826	139	0.1603	2610	X-RAY DIFFRACTION	100
2.4354-2.5329	0.1692	110	0.1624	2585	X-RAY DIFFRACTION	100
2.5329-2.6482	0.1968	141	0.1613	2578	X-RAY DIFFRACTION	100
2.6482-2.7878	0.1977	142	0.1682	2604	X-RAY DIFFRACTION	100
2.7878-2.9624	0.2141	142	0.1674	2581	X-RAY DIFFRACTION	100
2.9624-3.1911	0.2023	148	0.168	2550	X-RAY DIFFRACTION	100
3.1911-3.5122	0.173	138	0.1664	2621	X-RAY DIFFRACTION	100
3.5122-4.0203	0.1751	140	0.172	2568	X-RAY DIFFRACTION	100
4.0203-5.0645	0.1746	144	0.174	2579	X-RAY DIFFRACTION	100
5.0645-53.4294	0.2104	145	0.1977	2550	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	1.6306	-0.9008	0.3536	1.2837	-0.4449	1.0544	-0.13	0.5238	0.4027	-0.6327	0.074	-0.164	-0.2312	0.0879	-0.0233	0.4689	-0.0244	0.0302	0.3596	0.1228	0.289	-48.6144	48.6548	-44.5308
2	0.9895	0.0062	0.4583	0.8881	0.015	0.9337	-0.0065	0.0647	0.2026	-0.0195	0.0221	-0.1466	-0.2285	0.2816	-0.0041	0.1965	-0.0595	0.0211	0.2124	-0.0072	0.2427	-38.0255	44.2191	-19.7413
3	0.6888	0.408	0.1312	1.1412	0.5427	0.7858	0.0579	-0.2247	0.0465	0.3019	0.0769	-0.261	-0.013	0.3161	-0.0277	0.2401	-0.044	-0.0922	0.4256	-0.0468	0.2744	-27.6754	36.9335	-1.2037
4	0.9412	0.0472	0.0531	0.9045	0.0793	0.2349	0.027	-0.1017	-0.0846	0.0811	-0.0009	-0.1852	0.1076	0.2287	-0.025	0.1851	0.0356	-0.0225	0.2677	-0.0177	0.2499	-33.7419	23.6486	-14.3964
5	0.9884	0.1776	0.1053	0.9611	-0.0339	0.8715	0.0724	0.045	-0.0414	-0.0294	0.0307	-0.4409	0.0121	0.4635	-0.0754	0.1752	-0.0245	0.0103	0.4003	-0.041	0.3298	-23.6706	34.2809	-20.5662
6	2.2916	0.3369	1.1429	0.6067	-0.3718	1.0973	0.2028	-1.0131	0.2857	0.5376	-0.0552	-0.1392	-0.3065	-0.1209	-0.0992	0.676	-0.1469	-0.0221	0.6897	-0.214	0.4609	-40.7004	51.9218	9.043

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 183 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 184 through 221 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 222 through 330 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 331 through 408 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 409 through 455 )

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