PDB-9bky: Crystal structure of a C2 domain from Trichomonas vaginalis (sulf...

ID or keywords:

Entry

Database: PDB / ID: 9bky

Title

Crystal structure of a C2 domain from Trichomonas vaginalis (sulfate bound)

Components

XYPPX repeat family protein

Keywords

LIPID BINDING PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Trichomonas vaginalis / C2 domain

Function / homology

Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / calcium ion binding / membrane / XYPPX repeat family protein

Function and homology information

Biological species

Trichomonas vaginalis G3 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of a C2 domain from Trichomonas vaginalis (sulfate bound)
Authors: Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P.

History

Deposition	Apr 29, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bky.cif.gz	184.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9bky.ent.gz	147.4 KB	Display	PDB format
PDBx/mmJSON format	9bky.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bky_validation.pdf.gz	470.2 KB	Display	wwPDB validaton report
Full document	9bky_full_validation.pdf.gz	472.1 KB	Display
Data in XML	9bky_validation.xml.gz	19.8 KB	Display
Data in CIF	9bky_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bk/9bky ftp://data.pdbj.org/pub/pdb/validation_reports/bk/9bky	HTTPS FTP

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Related structure data

Similar structure data	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	#196 - Apr 2016 Lead Poisoning similarity (5) #148 - Apr 2012 Ras Protein similarity (5) #239 - Nov 2019 Phospholipase A2 similarity (5)

Deposited unit

A: XYPPX repeat family protein

B: XYPPX repeat family protein

C: XYPPX repeat family protein

hetero molecules

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

1

A: XYPPX repeat family protein

hetero molecules

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

2

B: XYPPX repeat family protein

hetero molecules

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

3

C: XYPPX repeat family protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.399, 86.399, 132.663
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-356- HOH

#1: Protein	XYPPX repeat family protein Mass: 15905.209 Da / Num. of mol.: 3 / Fragment: M1-E130 Source method: isolated from a genetically manipulated source Details: C2 domain / Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_347440 / Plasmid: TrvaA.17083.b.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2FNQ6
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.59 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Crystal Screen HT C8: 2.0M Ammonium Sulfate, TrvaA.17083.b.B2.PB00135 at 12 mg/mL. plate 13973 well C8, drop 1, Puck: PSL-0315, Cryo: 2.5M Lithium Sulfate.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 13, 2024
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.73→44.94 Å / Num. obs: 53166 / % possible obs: 100 % / Redundancy: 26.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.202 / R_pim(I) all: 0.04 / R_rim(I) all: 0.206 / Χ²: 1.01 / Net I/σ(I): 14.9 / Num. measured all: 1389460
Reflection shell	Resolution: 1.73→1.77 Å / % possible obs: 100 % / Redundancy: 27.4 % / R_merge(I) obs: 2.503 / Num. measured all: 105572 / Num. unique obs: 3860 / CC_1/2: 0.748 / R_pim(I) all: 0.484 / R_rim(I) all: 2.55 / Χ²: 1.06 / Net I/σ(I) obs: 2.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.21_5207: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.73→44.94 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2094	2597	4.89 %
R_work	0.1796	-	-
obs	0.1811	53062	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.73→44.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3185	0	112	271	3568

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3415
X-RAY DIFFRACTION	f_angle_d	1	4664
X-RAY DIFFRACTION	f_dihedral_angle_d	12.854	1210
X-RAY DIFFRACTION	f_chiral_restr	0.066	504
X-RAY DIFFRACTION	f_plane_restr	0.008	579

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 (%)
1.73-1.76	0.3436	122	0.291	2623	X-RAY DIFFRACTION	100
1.76-1.8	0.324	146	0.2707	2588	X-RAY DIFFRACTION	100
1.8-1.83	0.2621	126	0.2269	2628	X-RAY DIFFRACTION	100
1.83-1.87	0.23	128	0.2029	2611	X-RAY DIFFRACTION	100
1.87-1.92	0.2221	140	0.1872	2616	X-RAY DIFFRACTION	100
1.92-1.96	0.2276	121	0.1827	2634	X-RAY DIFFRACTION	100
1.96-2.02	0.2107	130	0.1853	2623	X-RAY DIFFRACTION	100
2.02-2.08	0.2269	144	0.1761	2624	X-RAY DIFFRACTION	100
2.08-2.14	0.2159	129	0.1675	2633	X-RAY DIFFRACTION	100
2.14-2.22	0.2023	121	0.169	2645	X-RAY DIFFRACTION	100
2.22-2.31	0.2091	135	0.1633	2627	X-RAY DIFFRACTION	100
2.31-2.41	0.2145	146	0.1629	2648	X-RAY DIFFRACTION	100
2.41-2.54	0.1947	164	0.1806	2628	X-RAY DIFFRACTION	100
2.54-2.7	0.2159	142	0.1884	2650	X-RAY DIFFRACTION	100
2.7-2.91	0.2297	113	0.2004	2688	X-RAY DIFFRACTION	100
2.91-3.2	0.2187	157	0.1816	2667	X-RAY DIFFRACTION	100
3.2-3.66	0.1912	135	0.1637	2703	X-RAY DIFFRACTION	100
3.66-4.61	0.1607	130	0.1431	2752	X-RAY DIFFRACTION	100
4.62-44.94	0.2118	168	0.1993	2877	X-RAY DIFFRACTION	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	1.1691	-0.088	-0.3056	0.3328	0.3428	0.3558	-0.0936	-0.2429	0.0553	0.342	0.0033	-0.1131	-0.1819	-0.2983	-0.0494	0.2077	0.0131	-0.04	0.1655	-0.0206	0.1536	-16.5338	-31.2514	-8.6717
2	3.3606	1.3613	0.6478	0.5539	0.136	0.2064	-0.266	0.5878	-0.2065	-0.5035	0.3187	-0.1399	-0.4203	0.2611	0.0481	0.3453	-0.004	0.0004	0.2066	0.0131	0.1705	-10.9222	-26.7696	-34.8379
3	0.1913	0.3339	-0.1909	0.5421	-0.1684	1.7092	0.1609	-0.0534	-0.1202	-0.1151	-0.0307	0.0637	0.434	-0.1768	0.0015	0.1655	0.0193	-0.0198	0.1287	-0.0047	0.1443	-13.0259	-34.2036	-17.6589
4	0.3205	0.4414	-0.0159	0.2509	0.1835	0.4837	0.0285	0.2464	-0.0837	0.0993	0.0819	-0.1217	0.3908	0.6646	-0.1725	0.1927	0.0649	-0.025	0.179	-0.0395	0.1494	-8.5597	-34.6809	-27.8097
5	1.1743	0.0419	0.418	0.4362	-0.3938	0.652	-0.0788	-0.0582	0.1271	0.0342	-0.0362	-0.0075	-0.3218	0.0118	-0.0442	0.1849	0.0226	-0.0096	0.1505	-0.0269	0.1569	-9.453	-24.7068	-11.531
6	0.1664	-0.0359	0.0476	0.2215	-0.066	-0.0175	0.1477	0.4819	0.4565	0.2049	-0.1757	-0.4082	-0.2802	0.2268	-0.002	0.1876	-0.0303	0.0244	0.2439	0.0858	0.2681	-2.4554	-22.1595	-25.6341
7	0.5156	-0.2293	0.1462	-0.0058	-0.1483	0.11	-0.1369	-0.2074	0.1325	0.058	0.0307	-0.0634	-0.2922	-0.1846	-0.0071	0.1998	0.0471	-0.0143	0.1941	-0.0213	0.1487	-15.9439	-26.3383	-10.1168
8	0.0248	0.0049	0.0229	-0.0054	-0.0075	0.0053	0.0924	-0.243	-0.397	-0.5093	0.2136	0.3666	-0.299	-0.0861	-0.0001	0.6968	0.1265	0.0801	0.9487	-0.0026	0.4614	-23.0124	-32.1706	-1.8595
9	0.4252	-0.1477	0.6855	0.2629	0.0124	0.8015	0.0407	-0.457	-0.1675	0.0362	0.0129	-0.1471	0.0643	-0.4487	0.0108	0.1903	-0.0544	-0.0332	0.1994	0.0322	0.217	-9.0031	-61.2145	0.6297
10	0.6928	0.0805	-0.7209	1.1821	-0.2068	0.7018	-0.015	0.094	-0.053	-0.345	0.1818	-0.2925	-0.3966	0.1537	0.1735	0.2057	-0.0148	0.0526	0.1555	-0.003	0.1967	-8.6714	-51.4198	-13.7239
11	0.3568	0.4265	0.0814	0.4024	0.0169	0.5714	0.055	0.2863	-0.2218	-0.5021	0.0413	-0.3634	0.5415	0.1644	0.0568	0.268	-0.0271	0.0531	0.16	-0.0203	0.2121	-11.1409	-59.6077	-17.1868
12	0.6448	0.0951	-0.0166	0.4191	-0.2699	0.4575	-0.0861	-0.1792	0.0527	-0.3766	-0.0413	-0.1267	-0.3405	-0.1907	-0.1141	0.179	0.0126	-0.0573	0.2307	-0.0169	0.2723	-5.9167	-55.3598	3.6743
13	1.3662	0.4966	0.4495	1.6186	0.7162	1.1895	-0.0246	-0.0432	0.2862	-0.4545	0.1742	-0.3567	-0.2048	-0.1187	-0.1998	0.1707	0.015	0.0683	0.1366	0.003	0.2086	-9.2804	-48.5549	-12.3183
14	0.2055	0.2084	0.1345	1.1561	0.2345	0.6349	0.1128	-0.8472	0.0766	0.1913	-0.1877	0.2184	0.0976	-0.1778	-0.2787	0.1867	-0.0715	0.0115	0.4344	0.0075	0.1792	-18.8787	-56.1002	2.9813
15	0.2022	0.0651	-0.2203	0.109	0.1049	0.2975	-0.0322	-0.0699	0.0268	-0.4219	0.2746	0.6595	0.0786	-0.0659	0.0023	0.1819	-0.0214	-0.0356	0.182	0.0127	0.3078	-20.4701	-44.0094	-12.4474
16	0.6192	0.8426	-0.1427	0.8218	-0.2921	1.1071	0.0651	-0.6867	-0.1535	0.226	-0.018	-0.1324	-0.0626	-0.5473	-0.1538	0.1943	-0.0811	-0.0391	0.2698	0.0839	0.1997	-13.3471	-62.9777	3.462
17	0.5431	0.0506	-0.1112	0.5806	-0.0742	-0.011	0.1367	-0.1902	0.239	0.1392	-0.0128	0.0464	-0.318	-0.0039	-0.0105	0.2009	-0.0401	0.0209	0.2209	-0.0277	0.173	6.0989	-24.557	-13.4458
18	0.0526	-0.0377	0.046	0.0139	0.0255	0.0613	-0.0317	0.2524	-0.0143	-0.7086	0.1709	-0.2682	-0.3683	0.2629	0.0013	0.3401	-0.0528	0.0515	0.2666	-0.0308	0.2065	17.6653	-36.0079	-44.333
19	0.1767	0.2292	0.197	0.3946	0.2771	0.2743	-0.029	-0.1404	-0.0167	0.0446	0.0765	0.2347	0.1916	-0.0673	0.0001	0.1369	-0.0125	0.0242	0.1564	-0.0005	0.1899	5.553	-34.3655	-28.0046
20	0.1979	-0.1602	0.0455	0.2233	-0.2219	0.1999	0.079	0.4608	0.176	-0.3117	-0.0404	0.0768	-0.2575	-0.0923	-0.0051	0.2185	-0.0432	0.0207	0.2179	0.0142	0.1819	12.9713	-27.0795	-39.5195
21	0.1488	0.4016	0.1751	0.4023	0.1106	0.1841	0.0059	0.0168	-0.1335	-0.0437	-0.0534	-0.0197	0.1747	0.2166	-0	0.1818	-0.011	0.0247	0.1552	0.0066	0.183	5.285	-31.5205	-18.9418
22	1.7328	-0.0643	-0.3581	1.6919	-0.1108	0.131	0.0812	-0.0598	-0.3056	-0.2557	0.1076	0.0866	-0.0917	0.0431	0.0094	0.1148	-0.0005	-0.0083	0.1447	-0.0114	0.2001	10.8193	-37.6365	-34.175
23	0.3558	-0.4498	-0.6067	0.8234	0.2771	0.3541	0.0041	-0.2954	0.1578	0.099	0.0627	-0.2181	0.1171	0.3763	-0.0392	0.2202	-0.0652	-0.0215	0.2944	-0.0101	0.1404	18.0887	-29.4169	-18.149
24	0.2459	0.0653	0.068	0.4908	-0.1589	0.0646	-0.202	0.068	-0.5277	-0.6347	0.2652	-0.8792	0.1292	0.3375	0.0101	0.2088	-0.0309	0.0776	0.1915	-0.051	0.3544	21.7517	-41.3842	-34.3539
25	0.4508	0.5324	-0.0311	1.0376	-0.1245	0.5861	0.3163	-0.2082	0.13	0.0914	-0.1302	-0.0005	-0.5705	0.197	0.1026	0.2222	-0.0586	0.0334	0.1713	-0.0233	0.171	12.2979	-22.8694	-18.2994

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 13 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 14 through 25 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 26 through 64 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 65 through 78 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 79 through 102 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 103 through 113 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 114 through 123 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 124 through 130 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid -1 through 13 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 14 through 38 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 39 through 51 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 52 through 64 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 65 through 86 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 87 through 102 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 103 through 113 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 114 through 130 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid -5 through 13 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 14 through 25 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 26 through 38 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 39 through 51 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 52 through 64 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 65 through 86 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 87 through 102 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 103 through 113 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 114 through 130 )

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