PDB-4y7s: Crystal Structure of the CFEM protein Csa2

ID or keywords:

Entry

Database: PDB / ID: 4y7s

Title

Crystal Structure of the CFEM protein Csa2

Components

Surface antigen protein 2

Keywords

HEME BINDING PROTEIN / CFEM /

hemoprotein / csa-2 / iron acquisition

Function / homology

Function and homology information

heme transmembrane transport / single-species biofilm formation on inanimate substrate / fungal-type cell wall / : / intracellular iron ion homeostasis /

heme binding / extracellular region /

metal ion binding
Similarity search - Function

Biological species

Candida albicans (yeast)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 2 Å

Authors

Dvir, H. / Weissman, Z. / Nasser, L. / Hiya, D. / Kornitzer, D.

Funding support

Israel, 4items

Organization	Grant number	Country
Marie Curie	330879	Israel
Israeli Ministry of Health's Chief Scientist Office		Israel
Russell Berrie Nanotechnology Institute - Technion		Israel
Lorry I. Lokey Interdiciplinary Center for Life Sciences and Engineering		Israel

Citation

Journal: Nat Microbiol / Year: 2016
Title: Structural basis of haem-iron acquisition by fungal pathogens.
Authors: Nasser, L. / Weissman, Z. / Pinsky, M. / Amartely, H. / Dvir, H. / Kornitzer, D.

History

Deposition	Feb 16, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 12, 2016	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4y7s.cif.gz	197.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4y7s.ent.gz	168.2 KB	Display	PDB format
PDBx/mmJSON format	4y7s.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/y7/4y7s ftp://data.pdbj.org/pub/pdb/validation_reports/y7/4y7s	HTTPS FTP

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Related structure data

Similar structure data	6ud0-d 3sp8-3 5j3w-2 4iua-3 1wos-d 7bpu-2 4a62-1 6gg9-2 4s0w-d 7bpu-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	#241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Surface antigen protein 2

B: Surface antigen protein 2

C: Surface antigen protein 2

hetero molecules

36.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	61.341, 61.208, 97.300
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	chain A	A	34 - 144
2	1	1	chain B	B	34 - 144
3	1	1	chain C	C	34 - 143

#1: Protein	Surface antigen protein 2 / Csa2 Mass: 11659.239 Da / Num. of mol.: 3 / Fragment: UNP residues 34-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Production host: Escherichia coli (E. coli) / Variant (production host): Origami / References: UniProt: Q5A0X8
#2: Chemical	ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE) Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃₄H₃₄FeN₄O₄
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.61 Å³/Da / Density % sol: 52.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein was mixed at ration of 2:1 with a reservoir (0.1M HEPES pH 7.5, 8% EG, 13.75% PEG 10,000)

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å

Detector

Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 2, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Redundancy: 15.1 % / Number: 370056 / R_merge(I) obs: 0.061 / Χ²: 0.93 / D res high: 2 Å / D res low: 40 Å / Num. obs: 24507 / % possible obs: 96

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	ID	R_merge(I) obs	Chi squared	Redundancy
5.42	40	1	0.027	1.088	15.5
4.31	5.42	1	0.03	1.08	16.5
3.76	4.31	1	0.031	0.806	16.8
3.42	3.76	1	0.039	0.879	16.9
3.17	3.42	1	0.048	0.871	16.8
2.99	3.17	1	0.062	0.899	16.9
2.84	2.99	1	0.084	0.926	16.8
2.71	2.84	1	0.102	0.919	16.9
2.61	2.71	1	0.13	0.944	16.8
2.52	2.61	1	0.159	0.922	16.8
2.44	2.52	1	0.17	0.907	16.8
2.37	2.44	1	0.21	0.933	16.9
2.31	2.37	1	0.245	0.916	16.6
2.25	2.31	1	0.282	0.911	16.5
2.2	2.25	1	0.336	0.952	16.2
2.15	2.2	1	0.376	0.922	13.9
2.11	2.15	1	0.38	0.9	10.7
2.07	2.11	1	0.431	0.897	8.6
2.03	2.07	1	0.548	0.903	7.2
2	2.03	1	0.625	0.853	5.4

Reflection

Resolution: 2→40 Å / Num. all: 25528 / Num. obs: 25528 / % possible obs: 96 % / Redundancy: 15.1 % / B_iso Wilson estimate: 24.36 Å² / R_merge(I) obs: 0.061 / R_pim(I) all: 0.016 / R_rim(I) all: 0.063 / Χ²: 0.927 / Net I/av σ(I): 43.511 / Net I/σ(I): 12.7 / Num. measured all: 370056

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2-2.03	5.4	0.625	2.04	850	0.774	0.275	0.688	0.853	67.5
2.03-2.07	7.2	0.548		944	0.866	0.207	0.589	0.903	75.6
2.07-2.11	8.6	0.431		1075	0.92	0.148	0.458	0.897	85.1
2.11-2.15	10.7	0.38		1169	0.944	0.118	0.399	0.9	95.3
2.15-2.2	13.9	0.376		1262	0.965	0.103	0.39	0.922	99.3
2.2-2.25	16.2	0.336		1240	0.979	0.085	0.347	0.952	99.4
2.25-2.31	16.5	0.282		1255	0.986	0.07	0.291	0.911	99.5
2.31-2.37	16.6	0.245		1265	0.989	0.061	0.253	0.916	99.5
2.37-2.44	16.9	0.21		1257	0.993	0.052	0.216	0.933	99.5
2.44-2.52	16.8	0.17		1243	0.995	0.042	0.175	0.907	99.8
2.52-2.61	16.8	0.159		1261	0.996	0.039	0.164	0.922	99.8
2.61-2.71	16.8	0.13		1271	0.996	0.032	0.134	0.944	99.8
2.71-2.84	16.9	0.102		1257	0.998	0.025	0.105	0.919	99.9
2.84-2.99	16.8	0.084		1273	0.998	0.021	0.086	0.926	100
2.99-3.17	16.9	0.062		1280	0.999	0.015	0.064	0.899	100
3.17-3.42	16.8	0.048		1296	0.999	0.012	0.05	0.871	100
3.42-3.76	16.9	0.039		1270	0.999	0.01	0.04	0.879	100
3.76-4.31	16.8	0.031		1311	0.999	0.008	0.032	0.806	100
4.31-5.42	16.5	0.03		1329	0.999	0.007	0.031	1.08	100
5.42-40	15.5	0.027		1399	1	0.007	0.028	1.088	99.3

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Phasing

Phasing

Method:

SAD

Phasing MAD set

Highest resolution: 2.5 Å / Lowest resolution: 40 Å

Phasing MAD set shell

ID	Resolution (Å)
1	13.91-40
1	8.42-13.91
1	6.04-8.42
1	4.71-6.04
1	3.86-4.71
1	3.27-3.86
1	2.83-3.27
1	2.5-2.83

Phasing MAD set site

Atom type symbol: Fe / Occupancy iso: 0

ID	B iso	Fract x	Fract y	Fract z	Occupancy
1	17.2907	-0.936	-0.941	-0.034	0.773
2	19.0361	-0.737	-1.158	-0.21	0.8
3	35.0787	-0.862	-1.003	-0.369	0.8
4	58.9315	-0.709	-0.989	-0.305	0.261
5	79.3633	-0.757	-0.941	-0.006	0.283

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	Reflection	Reflection acentric	Reflection centric
13.91-40	0.236	0.477	87	43	44
8.42-13.91	0.327	0.507	302	195	107
6.04-8.42	0.376	0.502	623	466	157
4.71-6.04	0.393	0.489	1073	862	211
3.86-4.71	0.413	0.493	1637	1373	264
3.27-3.86	0.368	0.427	2315	1993	322
2.83-3.27	0.279	0.318	3134	2748	386
2.5-2.83	0.192	0.214	4018	3597	421

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 24189

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.61-100	71.5	0.673	516
6-7.61	66.4	0.847	518
5.21-6	65.6	0.872	513
4.7-5.21	64	0.883	551
4.31-4.7	58.1	0.905	596
4.01-4.31	59.2	0.896	642
3.76-4.01	61.5	0.918	690
3.55-3.76	62.9	0.898	712
3.37-3.55	61.6	0.907	765
3.22-3.37	61.9	0.897	772
3.09-3.22	64.4	0.891	832
2.97-3.09	67.3	0.892	861
2.86-2.97	64.9	0.877	893
2.77-2.86	72.6	0.878	912
2.68-2.77	66.4	0.871	944
2.6-2.68	72	0.867	988
2.53-2.6	70.5	0.875	997
2.47-2.53	83.8	0.885	1031
2.4-2.47	89.2	0.868	1027
2.35-2.4	87.9	0.866	1085
2.29-2.35	90.5	0.87	1104
2.24-2.29	90.2	0.853	1123
2.2-2.24	91.4	0.827	1142
2.15-2.2	92.3	0.796	1179
2.11-2.15	89.1	0.736	1098
2.07-2.11	88.4	0.619	1015
2.04-2.07	89.7	0.592	887
2-2.04	92.9	0.466	796

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Processing

Software

Name	Version	Classification
HKL-3000		data reduction
SCALEPACK		data scaling
SHELX		phasing
MLPHARE		phasing
DM	6.3	phasing
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 2→28.672 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 19.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1916	2079	4.87 %	Random Selection
R_work	0.1526	40580	-	-
obs	0.1545	25528	89.03 %	-

Solvent computation

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

Displacement parameters

B_iso max: 127.79 Å² / B_iso mean: 36.0733 Å² / B_iso min: 12.72 Å²

Refinement step

Cycle: final / Resolution: 2→28.672 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2437	0	230	241	2908
B_iso mean	-	-	34.29	39.02	-
Num. residues	-	-	-	-	332

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	2671
X-RAY DIFFRACTION	f_angle_d	1.528	3693
X-RAY DIFFRACTION	f_chiral_restr	0.046	392
X-RAY DIFFRACTION	f_plane_restr	0.007	463
X-RAY DIFFRACTION	f_dihedral_angle_d	13.455	889

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	1814	X-RAY DIFFRACTION	20.341	TORSIONAL
1	2	B	1814	X-RAY DIFFRACTION	20.341	TORSIONAL
1	3	C	1814	X-RAY DIFFRACTION	20.341	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9989-2.0454	0.2279	61	0.2281	1045	1106	34
2.0454-2.0965	0.2071	67	0.1962	1533	1600	51
2.0965-2.1532	0.2392	102	0.1767	2094	2196	69
2.1532-2.2165	0.2261	117	0.1793	2700	2817	87
2.2165-2.2881	0.1697	165	0.1665	2886	3051	96
2.2881-2.3698	0.2365	138	0.1628	3046	3184	100
2.3698-2.4646	0.2113	162	0.159	2992	3154	100
2.4646-2.5767	0.2122	149	0.1639	3072	3221	100
2.5767-2.7125	0.1955	152	0.1623	3038	3190	100
2.7125-2.8823	0.2075	170	0.1605	3022	3192	100
2.8823-3.1046	0.2195	136	0.1613	3065	3201	100
3.1046-3.4166	0.2016	170	0.1644	3013	3183	100
3.4166-3.9099	0.1902	185	0.1425	2994	3179	100
3.9099-4.922	0.1708	150	0.1191	3037	3187	100
4.922-28.6751	0.1471	155	0.1401	3043	3198	100

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	3.2182	3.9964	-1.1562	5.0557	-2.0059	3.8493	-0.197	0.1176	0.2759	0.2405	0.1052	0.8455	-0.3578	-1.1266	0.0975	0.2523	0.0427	-0.0162	0.4453	-0.1396	0.2901	35.8032	-6.4909	-1.6079
2	4.2161	-2.6828	-0.2256	6.9324	-0.0392	1.7517	-0.0698	-0.0578	-0.2347	0.0212	-0.0076	0.0693	0.1733	-0.1688	0.0841	0.165	-0.0268	-0.0027	0.1993	-0.036	0.1128	45.7342	-11.6141	2.9466
3	5.6635	-2.7958	-3.7098	2.0562	0.4215	7.5649	-0.2452	-0.9684	-0.184	0.2589	0.2486	-0.1653	0.2287	0.4833	0.0557	0.154	0.0143	-0.0118	0.2296	-0.044	0.2175	54.8765	-8.9595	8.8987
4	2.41	1.0235	2.7164	2.7838	-0.7596	4.6273	-0.0772	0.0911	0.2911	-0.1384	-0.1264	-0.1044	-0.314	-0.0617	0.2023	0.1691	-0.0064	0.0009	0.1167	0.0071	0.1521	51.365	-1.6282	0.0102
5	7.9941	-0.0758	-4.2355	6.5094	0.8943	2.4082	-0.1195	-0.7719	0.4137	-0.1537	0.4891	-0.8974	-0.2312	1.1198	-0.3722	0.1891	-0.0569	-0.0198	0.339	-0.0336	0.2979	61.6271	-1.5926	8.0879
6	3.0472	-2.3786	-0.5269	4.6774	-1.815	1.8439	0.0284	0.348	0.8784	0.0322	-0.3398	-0.6123	-0.396	0.3197	0.3782	0.2664	-0.0124	-0.0267	0.2186	0.0656	0.3152	47.375	10.8087	14.4654
7	6.3409	0.1664	1.7109	4.6184	0.0341	2.8406	-0.0038	0.4493	0.779	-0.0515	-0.2937	0.2362	-0.4982	-0.3052	0.227	0.3493	0.0937	0.0014	0.231	-0.0125	0.3209	36.2813	15.0704	13.5101
8	5.097	-2.2324	0.1831	2.6662	-0.6676	4.3726	-0.0341	-0.3768	0.2401	0.0374	-0.1482	0.8	-0.3227	-0.5876	0.3107	0.3513	0.0347	0.0239	0.3053	-0.2081	0.5201	25.7617	13.2946	16.6163
9	4.766	0.0692	1.8785	2.543	-0.0569	2.2493	0.5033	0.0818	-0.4534	-0.0774	-0.4989	0.8679	0.3128	-0.3741	-0.0019	0.3158	0.0205	-0.0428	0.27	-0.1561	0.4057	28.8347	4.2716	14.3881
10	6.2615	5.605	-5.1632	5.0673	-4.5554	4.9313	0.006	-0.0798	-0.3524	-0.1286	-0.0069	-1.3445	0.7234	0.4102	0.0135	0.3631	0.1416	-0.0325	0.4398	-0.1411	0.4691	35.2027	6.1295	35.9924
11	7.3025	-5.0516	-0.3216	5.864	-2.0361	2.171	0.1287	-0.0405	-0.6392	-0.1736	0.0321	0.7463	-0.0097	-0.0358	-0.1302	0.221	-0.02	-0.0032	0.1822	-0.012	0.2882	39.4004	-4.4132	27.9601
12	7.9979	-4.7096	-5.5365	7.115	3.3397	3.9832	0.0851	0.86	-0.6535	-0.6043	-0.33	0.4508	0.5627	0.0215	0.2905	0.2663	0.0588	-0.0271	0.34	-0.0371	0.2401	48.6151	-8.8287	21.0813
13	1.5855	2.7626	-1.4414	7.1083	0.343	4.8636	0.01	1.0582	-1.2109	-0.8463	-0.2189	-0.7016	0.8322	0.6591	0.1732	0.3284	0.1957	-0.026	0.4807	-0.0987	0.3975	54.1554	-14.3095	24.4054
14	5.659	1.1254	2.8451	8.093	-0.9731	4.4417	-0.0887	-0.7645	-0.7543	0.6374	0.1738	0.0525	-0.17	-0.2921	-0.0569	0.2913	0.0027	0.0712	0.2489	0.0628	0.227	43.8556	-7.1726	34.9826
15	7.3741	-1.7766	-0.3632	7.6547	2.5242	0.8425	-0.0954	0.0028	-0.5765	0.4389	-0.2563	-0.5997	0.7498	0.8975	0.1718	0.3007	0.106	-0.0421	0.4598	0.1323	0.304	57.6089	-10.4768	32.3918
16	4.515	-3.1465	-1.4951	5.4549	1.1905	2.3157	0.0955	0.1561	0.1744	-0.1349	-0.4867	-0.6969	-0.0787	0.9058	0.1896	0.2297	0.006	0.0146	0.4395	0.1504	0.273	55.6847	-2.2293	24.0135
17	6.434	-0.4905	1.2757	2.5396	2.2029	3.6673	-0.169	-0.6563	0.5761	0.7151	-0.094	-0.4826	-0.4148	0.3684	0.2401	0.4162	-0.1128	-0.1259	0.2797	0.0154	0.2408	52.5276	3.3488	33.0276
18	3.9835	-1.1364	1.7085	0.7886	-0.0561	1.4032	-0.0287	0.0546	0.1367	0.0042	-0.0502	-0.1406	-0.0509	0.1538	-0	0.3215	-0.0979	-0.2823	0.7051	0.3381	0.7348	64.8392	-4.5556	32.8113

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 34 through 51 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 52 through 87 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 88 through 103 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 104 through 131 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 132 through 144 )	A
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 34 through 51 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 52 through 87 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 88 through 103 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 104 through 144 )	B
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 34 through 38 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 39 through 51 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 52 through 60 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 61 through 67 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 68 through 87 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 88 through 103 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 104 through 121 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 122 through 131 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 132 through 142 )	C

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