PDB-5o46: Crystal structure of Iristatin, a secreted salivary cystatin from...

ID or keywords:

Entry

Database: PDB / ID: 5o46

Title

Crystal structure of Iristatin, a secreted salivary cystatin from the hard tick Ixodes ricinus

Components

Iristatin

Keywords

hydrolase inhibitor /

cystatin /

protease inhibitor /

tick /

saliva

Function / homology

Cystatin domain / Cystatin-like domain /

Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / cysteine-type endopeptidase inhibitor activity / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Iristatin

Function and homology information

Biological species

Ixodes ricinus (castor bean tick)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.76 Å

Authors

Busa, M. / Rezacova, P. / Kotal, J. / Kotsyfakis, M. / Mares, M.

Funding support

Czech Republic, 7items

Organization	Grant number	Country
Czech Science Foundation	13-11043S	Czech Republic
Ministry of Education, Youth and Sports of the Czech Republic	InterBioMed LO1302	Czech Republic
INSTITUTE OF ORGANIC CHEMISTRY AND BIOCHEMISTRY AS CR V.V.I.	RVO 61388963	Czech Republic
Institute of Parasitology, the Czech Academy of Sciences	RVO 60077344	Czech Republic
Czech Science Foundation	P502/12/2409	Czech Republic
Grant Agency of the University of South Bohemia in Ceske Budejovice	038/2016/P	Czech Republic
European Union	Marie Curie Reintegration grant PIRG07-GA-2010-268177

Citation

Journal: Cell.Mol.Life Sci. / Year: 2019
Title: The structure and function of Iristatin, a novel immunosuppressive tick salivary cystatin.
Authors: Kotal, J. / Stergiou, N. / Busa, M. / Chlastakova, A. / Berankova, Z. / Rezacova, P. / Langhansova, H. / Schwarz, A. / Calvo, E. / Kopecky, J. / Mares, M. / Schmitt, E. / Chmelar, J. / Kotsyfakis, M.

History

Deposition	May 26, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 13, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jun 26, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 17, 2024	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	5o46.cif.gz	118.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5o46.ent.gz	92.6 KB	Display	PDB format
PDBx/mmJSON format	5o46.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/o4/5o46 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/5o46	HTTPS FTP

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Related structure data

Related structure data	3l0rS S: Starting model for refinement
Similar structure data	7nqi-d 3l0r-2 3k6g-1 5xhe-d 3l0r-1 6y0e-2 3iqt-d 2zez-3 7nqj-d 4lw9-9 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#224 - Aug 2018 Legumain similarity (3)

Deposited unit

B: Iristatin

A: Iristatin

hetero molecules

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

1

B: Iristatin

hetero molecules

defined by author
Evidence: homology
13.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Iristatin

hetero molecules

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

Unit cell

Length a, b, c (Å)	39.033, 76.929, 92.122
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Iristatin Mass: 13850.943 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ixodes ricinus (castor bean tick) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3B6UEB6*PLUS
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: 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: 2.5 Å³/Da / Density % sol: 50.73 %
Crystal grow	Temperature: 288.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-Tris buffer, pH 5.5 1 M ammonium sulphate 1% (w/v) PEG 3350 mother liquor: protein ratio 1.5:1

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.76→59.05 Å / Num. obs: 27677 / % possible obs: 97.84 % / Redundancy: 3.73 % / B_iso Wilson estimate: 36.75 Å² / CC_1/2: 1 / R_merge(I) obs: 0.038 / R_pim(I) all: 0.044 / Net I/σ(I): 19.32
Reflection shell	Resolution: 1.76→1.87 Å / Redundancy: 3.69 % / R_merge(I) obs: 0.71 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 4357 / CC_1/2: 0.76 / R_pim(I) all: 0.83 / % possible all: 96.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3L0R

3l0r

Resolution: 1.76→59.05 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.934 / SU B: 8.634 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25572	1384	5 %	RANDOM
R_work	0.19089	-	-	-
obs	0.1941	26286	97.84 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 41.036 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	-0 Å²	-0 Å²
2-	-	-0 Å²	0 Å²
3-	-	-	0.01 Å²

Refinement step

Cycle: 1 / Resolution: 1.76→59.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1858	0	18	241	2117

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	2000
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1857
X-RAY DIFFRACTION	r_angle_refined_deg	1.722	1.95	2723
X-RAY DIFFRACTION	r_angle_other_deg	0.947	3	4324
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.71	5	245
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.489	23.333	87
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.639	15	358
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.676	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	297
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	2174
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	417
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.997	1.29	936
X-RAY DIFFRACTION	r_mcbond_other	0.972	1.284	935
X-RAY DIFFRACTION	r_mcangle_it	1.757	1.923	1174
X-RAY DIFFRACTION	r_mcangle_other	1.761	1.93	1175
X-RAY DIFFRACTION	r_scbond_it	0.79	1.45	1064
X-RAY DIFFRACTION	r_scbond_other	0.788	1.45	1064
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.282	2.124	1542
X-RAY DIFFRACTION	r_long_range_B_refined	7.486	17.228	2288
X-RAY DIFFRACTION	r_long_range_B_other	7.485	17.264	2289
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.76→1.805 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.373	100	-
R_work	0.373	1890	-
obs	-	-	97.79 %

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	9.6684	0.4894	-2.433	8.56	-1.3287	43.3599	0.2036	0.0478	0.8799	0.3691	0.03	0.0325	-2.8435	-2.3516	-0.2337	0.3889	0.1167	0.0338	0.2079	0.0611	0.3486	11.18	30.639	7.544
2	0.4205	0.3368	-1.1303	11.0975	-14.9699	21.8774	0.0968	-0.1262	-0.1392	-0.3973	-0.3205	-0.3085	0.2035	0.5799	0.2237	0.166	0.0033	0.0338	0.235	0.069	0.3387	17.723	18.04	2.979
3	1.172	0.243	0.4679	3.7357	-1.2646	4.7868	0.0022	0.0263	-0.0411	0.1448	-0.0881	-0.1311	0.0304	0.1158	0.0858	0.1648	0.0229	-0.0001	0.0493	0.0137	0.1859	7.904	7.696	13.246
4	3.962	3.9447	0.5835	6.4957	1.1667	1.5764	0.1191	-0.0776	0.2759	0.2028	-0.1259	0.027	-0.1566	0.1245	0.0067	0.1608	-0.005	0.0002	0.0899	0.0403	0.227	10.012	20.277	8.59
5	7.1882	2.723	-1.2009	6.9384	-0.5634	0.5636	0.3218	-0.1541	-0.5039	0.5242	-0.3557	-0.6517	0.3036	0.272	0.034	0.4707	0.171	-0.0697	0.2232	0.0039	0.2698	9.727	-2.04	13.817
6	13.141	5.883	11.5989	25.648	4.3235	15.2252	0.4891	1.3838	-0.2436	-1.0821	-0.4576	-2.1654	1.1919	1.3932	-0.0315	0.3244	0.1642	0.0853	0.2829	0.0686	0.4468	15.464	0.504	7.343
7	2.3787	-0.2015	-0.1234	3.544	-0.4184	2.4345	0.0636	0.0911	-0.0272	-0.0638	-0.1962	0.1912	0.2876	-0.0377	0.1327	0.1905	0.0026	0.0166	0.0852	0.0515	0.1619	3.973	8.843	6.728
8	54.3592	7.0011	0.9049	10.6366	1.944	4.5654	-0.0967	-0.517	0.4658	0.8923	-0.0745	-1.5033	-0.4071	1.0291	0.1712	0.311	-0.1155	-0.1334	0.282	0.089	0.4169	16.566	19.748	18.325
9	12.5173	0.9468	16.8403	1.8849	3.0109	25.3889	0.2457	-1.0417	-0.1602	-0.0859	-0.2179	0.3987	-0.0258	-1.0454	-0.0278	0.2241	-0.0925	0.0541	0.3192	-0.0292	0.2996	-0.854	14.759	12.312
10	5.4514	-2.6172	-4.3887	9.5351	-3.8649	9.1713	0.1268	0.4659	0.0174	-0.7248	0.145	0.6289	0.8771	-1.3586	-0.2718	0.3329	-0.2399	-0.0157	0.4851	-0.0322	0.3468	-6.295	7.811	2.617
11	50.0466	27.5792	15.2256	31.4323	15.8513	30.7207	0.9659	1.1558	-4.5779	-0.0299	1.166	-2.9368	3.3798	-0.286	-2.1319	0.7572	-0.1649	-0.141	0.0931	-0.0478	0.7725	7.548	-12.594	32.097
12	5.1862	3.2741	0.2869	10.7533	-3.611	9.6578	0.0088	-0.3523	-0.1165	0.4469	0.0142	0.0727	0.0513	-0.804	-0.0229	0.2236	-0.021	-0.0175	0.1749	0.0084	0.1883	10.177	1.358	42.248
13	4.0932	-1.9456	3.9372	4.3176	-4.8828	8.9338	0.0301	-0.0138	-0.0057	0.0708	-0.0837	-0.1125	-0.1483	0.1455	0.0536	0.1593	-0.0186	0.0168	0.0678	-0.0022	0.1846	8.046	9.522	30.395
14	2.2555	-1.2632	1.3795	2.6105	-1.45	3.8805	0.0326	-0.1542	-0.1401	-0.019	0.0103	0.1569	0.0326	-0.2578	-0.043	0.1548	-0.0631	-0.0029	0.1569	0.0097	0.1939	4.257	6.239	31.271
15	11.6057	-8.9314	-0.799	8.8344	0.5818	4.4252	0.1351	0.0095	-0.0782	0.0306	-0.0456	0.0924	0.303	-0.401	-0.0896	0.1642	-0.0581	-0.0195	0.0761	0.0395	0.1917	5.227	1.335	33.266
16	21.2859	11.0341	-13.8668	23.1352	-9.5234	9.7574	0.3392	-0.1862	0.6065	0.254	-0.0601	0.503	-0.626	-0.0561	-0.2792	0.4331	0.1176	-0.0543	0.1513	-0.0461	0.2897	0.315	21.084	28.971
17	10.0355	-2.1748	3.9947	8.754	1.1324	15.5031	-0.5016	-0.6005	0.8629	0.9373	0.2519	-0.3672	-1.5957	-0.0172	0.2498	0.5243	0.0272	-0.0545	0.1771	-0.0554	0.4023	4.737	21.691	33.481
18	11.3466	-3.564	0.3018	3.9584	-0.6364	2.0806	-0.04	-0.6078	0.5025	0.1079	0.1155	0.0657	-0.0039	-0.329	-0.0754	0.1736	-0.0412	0.0009	0.2226	0.0078	0.2272	0.846	6.716	31.289
19	30.1488	-2.9693	12.9665	2.8541	-1.2485	6.9338	-0.1013	1.103	0.0065	-0.2688	-0.1867	-0.6303	0.0627	1.1564	0.288	0.2448	0.0056	0.0478	0.4155	0.1351	0.3525	18.205	1.52	27.087
20	3.2369	-2.6189	1.7011	3.2384	-2.5632	3.3516	0.048	-0.1364	0.0071	0.0609	0.1668	0.5646	0.0399	-0.5468	-0.2147	0.1996	-0.0464	0.027	0.3483	-0.0259	0.4633	-6.256	7.298	28.351

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	1 - 8
2	X-RAY DIFFRACTION	2	B	9 - 17
3	X-RAY DIFFRACTION	3	B	18 - 38
4	X-RAY DIFFRACTION	4	B	39 - 61
5	X-RAY DIFFRACTION	5	B	62 - 72
6	X-RAY DIFFRACTION	6	B	73 - 76
7	X-RAY DIFFRACTION	7	B	77 - 92
8	X-RAY DIFFRACTION	8	B	93 - 104
9	X-RAY DIFFRACTION	9	B	105 - 109
10	X-RAY DIFFRACTION	10	B	110 - 114
11	X-RAY DIFFRACTION	11	A	1 - 6
12	X-RAY DIFFRACTION	12	A	7 - 15
13	X-RAY DIFFRACTION	13	A	16 - 29
14	X-RAY DIFFRACTION	14	A	30 - 50
15	X-RAY DIFFRACTION	15	A	51 - 59
16	X-RAY DIFFRACTION	16	A	60 - 66
17	X-RAY DIFFRACTION	17	A	67 - 80
18	X-RAY DIFFRACTION	18	A	81 - 93
19	X-RAY DIFFRACTION	19	A	94 - 104
20	X-RAY DIFFRACTION	20	A	105 - 113

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