PDB-9zk6: Crystal structure of a C2 domain containing protein from Trichomo...

ID or keywords:

Entry

Database: PDB / ID: 9zk6

Title

Crystal structure of a C2 domain containing protein from Trichomonas vaginalis in complex with pyrophosphate

Components

C2 domain containing protein

Keywords

LIPID BINDING PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / 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 / PYROPHOSPHATE / C2 domain containing protein

Function and homology information

Biological species

Trichomonas vaginalis G3 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

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 containing protein from Trichomonas vaginalis in complex with pyrophosphate
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Buchko, G.W.

History

Deposition	Dec 5, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 17, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9zk6.cif.gz	119.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9zk6.ent.gz	92.4 KB	Display	PDB format
PDBx/mmJSON format	9zk6.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/zk/9zk6 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/9zk6	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: C2 domain containing protein

B: C2 domain containing protein

hetero molecules

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

1

A: C2 domain containing 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: C2 domain containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	35.518, 89.297, 96.105
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	C2 domain containing protein Mass: 16382.914 Da / Num. of mol.: 2 / Fragment: residues 1-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_002900 / Plasmid: TrvaA.01422.c.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2EZR3
#2: Chemical	ChemComp-PPV / PYROPHOSPHATE Mass: 177.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₄O₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	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: 2.32 Å³/Da / Density % sol: 46.95 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Pproplex C9: 0.1 M Sodium cacodylate pH 5.5, 20% PEG 4000. TrvaA.01422.c.B2.PB00149 at 20 mg/mL. overnight soak with 10mM pyrophosphate, plate 20301 C9 drop 1, Puck: PSL-0402, Cryo: 33% PEG 4000, 0.1M MES 5.5

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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: Sep 20, 2025
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: 1.7→48.05 Å / Num. obs: 34553 / % possible obs: 100 % / Redundancy: 13.2 % / CC_1/2: 0.999 / R_merge(I) obs: 0.042 / R_pim(I) all: 0.012 / R_rim(I) all: 0.044 / Χ²: 1.09 / Net I/σ(I): 25.7 / Num. measured all: 454670
Reflection shell	Resolution: 1.7→1.74 Å / % possible obs: 100 % / Redundancy: 13.7 % / R_merge(I) obs: 1.775 / Num. measured all: 34268 / Num. unique obs: 2497 / CC_1/2: 0.922 / R_pim(I) all: 0.493 / R_rim(I) all: 1.844 / Χ²: 0.9 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5765: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.7→48.05 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2312	1674	4.87 %
R_work	0.211	-	-
obs	0.212	34371	99.61 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→48.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2012	0	9	105	2126

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2065
X-RAY DIFFRACTION	f_angle_d	0.825	2809
X-RAY DIFFRACTION	f_dihedral_angle_d	12.416	779
X-RAY DIFFRACTION	f_chiral_restr	0.059	324
X-RAY DIFFRACTION	f_plane_restr	0.007	350

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 (%)
1.7-1.75	0.3712	131	0.3492	2680	X-RAY DIFFRACTION	99
1.75-1.81	0.4306	131	0.3407	2664	X-RAY DIFFRACTION	99
1.81-1.87	0.438	140	0.362	2692	X-RAY DIFFRACTION	100
1.87-1.95	0.3599	143	0.2785	2639	X-RAY DIFFRACTION	99
1.95-2.03	0.2838	161	0.238	2661	X-RAY DIFFRACTION	99
2.03-2.14	0.2854	162	0.2421	2681	X-RAY DIFFRACTION	100
2.14-2.28	0.2617	129	0.2444	2716	X-RAY DIFFRACTION	100
2.28-2.45	0.2518	138	0.2275	2707	X-RAY DIFFRACTION	100
2.45-2.7	0.2684	137	0.2269	2747	X-RAY DIFFRACTION	100
2.7-3.09	0.2321	123	0.2277	2776	X-RAY DIFFRACTION	100
3.09-3.89	0.2416	108	0.1998	2830	X-RAY DIFFRACTION	100
3.89-48.05	0.1733	171	0.1731	2904	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	0.0031	-0.0224	-0.0226	0.0959	0.1292	0.1509	-0.1713	0.6688	0.1342	-0.8146	0.1286	-0.1071	-0.477	-0.4065	-0.0091	0.6626	-0.0994	0.1137	0.51	-0.0121	0.4257	5.3231	-17.6704	-23.4218
2	0.4093	-0.1331	-0.2562	0.0939	0.0901	0.1409	-0.3424	-0.6275	-0.1816	0.1764	0.0347	0.2878	0.2088	-0.564	0.0001	0.5863	0.0286	0.0785	0.5271	0.0222	0.4624	-2.6015	-25.6512	-1.131
3	0.0529	-0.0528	-0.0175	0.0189	-0.0036	0.0759	0.0102	-0.0178	-0.1098	-0.3867	-0.1299	0.1823	0.4063	-0.2638	-0.0001	0.3845	0.0081	0.0392	0.4243	-0.0489	0.4307	9.0526	-25.3736	-15.7524
4	0.0265	-0.0649	0.0419	0.1089	-0.0872	0.0509	0.4023	-0.0976	-0.0796	-0.3061	-0.4148	-0.395	-0.0875	0.2776	0.0002	0.597	0.0123	0.1703	0.5736	-0.0198	0.615	14.8881	-26.5921	-19.3105
5	0.1264	0.035	-0.1404	0.2391	0.1245	0.1955	-0.0246	-0.2405	0.3459	0.2271	0.059	0.0199	-0.3849	-0.3545	-0	0.3277	-0.0225	-0.0174	0.4266	-0.0058	0.4118	2.0712	-17.5821	-7.2985
6	1.0301	-0.6422	1.0939	0.6789	-0.252	1.9133	-0.398	0.2364	0.1743	-0.3628	0.1209	-0.0978	-0.5209	-0.0741	-0.4362	0.5253	-0.1646	0.253	0.5112	-0.0169	0.5179	11.2373	-16.9308	-22.1856
7	0.0001	-0.0515	0.0406	0.4792	-0.1889	0.0773	-0.0168	-0.067	-0.1848	-0.422	0.1413	-0.1076	0.3091	-0.0655	-0.0002	0.6193	-0.0372	0.0554	0.4233	-0.0488	0.5053	8.2077	-28.1296	-23.9269
8	0.1404	0.0135	0.0902	0.0095	0.0357	0.0869	-0.5525	0.1434	0.6747	-0.3597	0.0935	0.3237	-0.2203	-0.7209	0.0031	0.366	0.0053	-0.0384	0.4767	0.0141	0.5223	10.0176	-27.7438	-0.2071
9	0.4277	-0.2005	-0.1202	0.451	0.236	0.1222	0.133	0.2113	-0.3342	-0.1209	-0.3937	0.2423	0.6731	0.321	-0.0001	0.7484	-0.0124	0.0198	0.4063	-0.0636	0.4227	2.715	-29.8266	-20.4957
10	0.6525	-0.3495	0.3413	0.1874	-0.1976	0.2328	0.1497	0.708	-0.1866	-0.9539	-0.2711	0.6706	-0.506	-1.2646	-0.0484	0.8096	0.1132	-0.0063	0.4738	-0.0419	0.3403	-1.6311	-19.9524	-27.5886
11	0.1406	0.0175	0.0678	0.0466	0.0309	0.0361	0.1969	0.3178	-0.2304	0.0176	0.2259	-0.0355	0.4773	-0.3361	0.0071	0.6143	-0.0894	-0.0085	0.3683	-0.0296	0.5597	-3.2824	-33.8983	-10.2747
12	0.0302	0.0343	-0.2431	0.0179	-0.222	1.8564	-0.1847	0.4826	-0.3381	-0.8933	-0.2521	-0.0499	-0.263	-0.5708	-0.0638	0.6005	0.0274	0.0798	0.448	0.022	0.4462	2.8869	-18.1635	-25.5111
13	0.9696	-0.232	-0.743	2.2236	-1.4171	1.5989	0.2894	0.028	-0.1417	0.0727	0.0517	0.0842	-0.1932	0.0531	0.0005	0.3875	0.0006	0	0.3804	0.0273	0.4097	-7.2164	-1.679	-14.6339
14	2.2085	0.6186	0.8798	0.5599	-0.1936	0.8571	0.1577	0.4132	-0.1309	0.1358	0.0848	0.0265	-0.3801	0.5104	0.1775	0.487	-0.0574	0.0234	0.403	0.0612	0.3377	-3.8538	0.6647	-15.9421
15	0.635	-0.2279	0.6083	0.381	-0.1153	0.533	0.3394	-0.4036	0.1258	0.2979	0.0993	-0.1928	-1.7322	0.9171	-0.0115	0.8469	-0.1397	0.0547	0.6128	-0.0551	0.4324	-2.2215	5.351	-0.1033
16	0.3428	0.109	0.0076	0.0335	-0.0087	0.0094	0.1682	-0.0942	0.038	0.0765	0.1301	0.6984	-0.7998	-0.2545	-0.0006	0.5156	0.0485	0.0757	0.4606	0.0276	0.5067	-9.9943	4.0869	-12.1444
17	0.0303	0.0266	0.0239	0.0626	-0.0454	0.1018	-0.4163	0.2803	-0.2037	-0.1233	-0.0461	0.0769	-0.2326	0.0281	0.0005	0.7735	-0.0128	0.1008	0.6118	0.0351	0.6122	-7.0535	5.8006	-28.0307
18	0.3519	0.2467	0.1114	0.3065	0.0614	0.0412	0.0136	0.0548	-0.0474	0.5153	0.2331	0.6871	-0.7876	-0.5356	0.0001	0.6307	0.0756	0.1807	0.5015	0.0511	0.5683	-12.9759	2.6656	-7.1592
19	1.0293	-0.5139	-0.1058	0.5161	0.2468	0.244	0.2969	0.0624	-0.3827	0.9851	0.0438	0.7321	0.5605	0.1273	0.0746	0.5281	0.006	0.0632	0.3966	0.0742	0.37	-7.561	-6.4897	0.2889
20	0.9469	-0.2553	0.8333	0.5687	-0.5613	0.9503	0.0836	0.1228	0.3286	-0.0922	0.19	0.5398	-0.3324	-1.0428	0.8082	-0.2187	0.3985	0.0723	0.7827	0.3618	0.8764	-20.238	0.2037	-17.1877
21	0.0789	0.0766	-0.1608	0.305	-0.3396	0.4097	0.1161	-0.3936	-0.1217	0.9582	0.1351	0.2748	0.4171	-0.1592	0.0009	0.462	0.0115	0.0157	0.4131	-0.0028	0.3884	-4.3385	-4.5286	-2.7182

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 12 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 13 through 24 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 25 through 31 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 32 through 39 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 40 through 52 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 53 through 58 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 59 through 73 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 74 through 80 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 81 through 92 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 93 through 104 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 105 through 115 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 116 through 126 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 31 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 32 through 52 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 53 through 65 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 66 through 73 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 74 through 80 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 81 through 92 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 93 through 104 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 105 through 115 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 116 through 125 )

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