PDB-9zk2: Crystal structure of a calcium bound C2 domain containing protein...

ID or keywords:

Entry

Database: PDB / ID: 9zk2

Title

Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (orthorhombic P form)

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 / C2 domain containing protein

Function and homology information

Biological species

Trichomonas vaginalis G3 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.53 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 calcium bound C2 domain containing protein from Trichomonas vaginalis (orthorhombic P form)
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	9zk2.cif.gz	129 KB	Display	PDBx/mmCIF format
PDB format	pdb9zk2.ent.gz	99.1 KB	Display	PDB format
PDBx/mmJSON format	9zk2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9zk2_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	9zk2_full_validation.pdf.gz	2.7 MB	Display
Data in XML	9zk2_validation.xml.gz	16.4 KB	Display
Data in CIF	9zk2_validation.cif.gz	21.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zk/9zk2 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/9zk2	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

33.2 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
16.5 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
16.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	35.507, 88.086, 97.040
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-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 179 / 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: 46.89 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Proplex A9: 0.2M NaCl, 0.1M MES, pH 6.0, 20% PEG2000 MME . TrvaA.01422.c.B2.PB00149 at 20 mg/mL. cocrystallization with 3.3 mM CaCl2 and phytic acid. The latter did not bind. plate 20301 A9 ...Details: Proplex A9: 0.2M NaCl, 0.1M MES, pH 6.0, 20% PEG2000 MME . TrvaA.01422.c.B2.PB00149 at 20 mg/mL. cocrystallization with 3.3 mM CaCl2 and phytic acid. The latter did not bind. plate 20301 A9 drop 3, Puck: PSL-0106, Cryo: 20% PEG200 + 80% crystallant

Crystal

Density Matthews: 2.32 Å³/Da / Density % sol: 46.89 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Proplex A9: 0.2M NaCl, 0.1M MES, pH 6.0, 20% PEG2000 MME . TrvaA.01422.c.B2.PB00149 at 20 mg/mL. cocrystallization with 3.3 mM CaCl2 and phytic acid. The latter did not bind. plate 20301 A9 ...

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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: 1.53→48.52 Å / Num. obs: 46936 / % possible obs: 100 % / Redundancy: 13 % / CC_1/2: 1 / R_merge(I) obs: 0.055 / R_pim(I) all: 0.016 / R_rim(I) all: 0.057 / Χ²: 1.02 / Net I/σ(I): 20.7 / Num. measured all: 611835
Reflection shell	Resolution: 1.53→1.57 Å / % possible obs: 100 % / Redundancy: 13.8 % / R_merge(I) obs: 1.524 / Num. measured all: 47335 / Num. unique obs: 3426 / CC_1/2: 0.877 / R_pim(I) all: 0.421 / R_rim(I) all: 1.582 / Χ²: 0.69 / 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: 1.53→48.52 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.75 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2558	2311	4.94 %
R_work	0.2281	-	-
obs	0.2296	46817	99.87 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.53→48.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2080	0	20	179	2279

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2158
X-RAY DIFFRACTION	f_angle_d	0.942	2939
X-RAY DIFFRACTION	f_dihedral_angle_d	15.14	796
X-RAY DIFFRACTION	f_chiral_restr	0.061	346
X-RAY DIFFRACTION	f_plane_restr	0.011	370

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 (%)
1.53-1.56	0.3896	122	0.3693	2596	X-RAY DIFFRACTION	100
1.56-1.6	0.3959	132	0.326	2562	X-RAY DIFFRACTION	100
1.6-1.63	0.3599	128	0.3001	2574	X-RAY DIFFRACTION	100
1.63-1.67	0.3746	128	0.2974	2607	X-RAY DIFFRACTION	100
1.67-1.72	0.3346	131	0.2763	2564	X-RAY DIFFRACTION	100
1.72-1.77	0.3271	131	0.2822	2591	X-RAY DIFFRACTION	100
1.77-1.83	0.3358	129	0.2999	2590	X-RAY DIFFRACTION	100
1.83-1.89	0.3226	130	0.2843	2596	X-RAY DIFFRACTION	100
1.89-1.97	0.2885	146	0.2442	2587	X-RAY DIFFRACTION	100
1.97-2.06	0.297	114	0.2441	2636	X-RAY DIFFRACTION	100
2.06-2.16	0.309	161	0.2464	2563	X-RAY DIFFRACTION	100
2.16-2.3	0.216	138	0.2379	2625	X-RAY DIFFRACTION	100
2.3-2.48	0.3106	153	0.2446	2598	X-RAY DIFFRACTION	100
2.48-2.73	0.2558	134	0.2428	2669	X-RAY DIFFRACTION	100
2.73-3.12	0.2884	139	0.2373	2630	X-RAY DIFFRACTION	100
3.12-3.93	0.2191	145	0.2108	2689	X-RAY DIFFRACTION	100
3.93-48.52	0.2109	150	0.1879	2829	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	0.9628	-0.3755	-0.278	0.1742	-0.062	0.3465	-0.0584	0.0077	-0.4888	-1.1164	-0.0978	-0.0215	-0.0915	-0.0637	0.0484	0.6454	-0.0328	0.168	0.292	-0.0152	0.2864	5.6898	-17.1204	-23.3004
2	0.0175	-0.264	0.0162	1.4286	0.2731	0.1318	-0.0046	-0.004	-0.2671	-0.3099	0.0716	0.1481	0.038	-0.102	-0.0636	0.1691	-0.0058	0.0152	0.3271	0.0267	0.3182	0.7078	-25.3229	-6.2965
3	0.0125	-0.0503	-0.0051	0.0744	-0.007	0.216	0.0167	0.1313	-0.2089	-0.5077	-0.1494	-0.2834	0.4003	0.0159	-0.0084	0.3595	0.0235	0.1562	0.3123	-0.023	0.436	13.4642	-23.8075	-16.0002
4	0.424	-0.0853	-0.1857	0.8876	0.6666	0.524	0.0893	-0.2028	0.3276	-0.1175	0.1011	0.1337	-0.2663	-0.1738	0.0422	0.0756	-0.0045	0.0069	0.3335	0.047	0.2741	0.0861	-17.1743	-6.6955
5	0.4977	-0.0863	-0.3639	0.0849	0.0791	0.4233	-0.1661	-0.0577	-0.1327	-0.8516	0.1255	-0.1578	0.2718	0.2548	0.4753	0.78	-0.0413	0.3173	0.3113	-0.0409	0.3864	11.8385	-21.8348	-27.0381
6	0.0249	-0.0348	-0.1408	0.2724	0.0368	0.411	-0.0753	-0.1901	-0.5397	-0.4704	0.1583	-0.0603	0.1438	-0.1056	0.0169	0.3096	-0.0281	0.1001	0.3108	-0.0125	0.3716	5.6543	-27.5841	-15.4943
7	0.0848	-0.1368	0.1369	0.2792	-0.2662	0.3031	0.0057	-0.173	0.2903	-0.2655	0.036	0.0054	0.1909	-0.0127	0.0208	0.1407	0.0074	-0.0106	0.3342	0.0811	0.388	8.942	-27.2822	0.3024
8	1.7418	0.0824	-0.0913	0.0569	-0.2244	1.1873	0.0374	-0.0041	-0.3136	-0.71	0.0565	0.0445	0.269	0.327	0.0596	0.6407	0.0209	0.0144	0.2437	-0.0289	0.3108	2.7295	-29.1844	-20.5048
9	1.2309	-0.4992	0.4851	0.1848	-0.1935	0.2153	0.3289	0.2978	-0.5348	-1.0451	-0.2686	0.3372	0.0478	-0.2697	0.1721	0.8052	0.0099	0.0186	0.3193	-0.0736	0.237	-0.9387	-19.2843	-27.9056
10	0.3523	-0.4408	0.307	0.8161	-0.533	1.0742	-0.0712	0.2464	-0.3206	-0.9286	0.1594	0.1735	-0.0251	-0.0482	0.0389	0.5062	-0.0426	0.0491	0.3318	0.0042	0.376	-0.34	-24.6387	-18.7734
11	0.1094	0.1775	0.0051	0.275	0.0117	-0.0069	-0.2896	-0.0649	0.0902	-0.3894	-0.4752	-0.3467	-0.2664	0.3532	-0.58	1.1904	-0.2089	0.5468	0.3862	0.1293	0.3895	9.6879	-10.2391	-31.4278
12	1.256	-0.7467	0.3082	0.5519	-0.4177	0.644	0.5139	-0.496	0.056	0.8735	-0.2777	0.3906	-0.2306	0.1672	0.1973	0.5641	-0.2225	-0.0062	0.4559	0.09	0.337	-3.8104	-2.2036	-5.0233
13	1.8065	-0.0399	0.5146	0.1864	-0.277	0.2488	0.651	0.4223	-0.6981	0.1288	0.4325	0.2437	0.0139	-0.3174	0.7945	0.5708	-0.0571	-0.0808	0.3327	0.0993	0.3599	-11.3308	-0.5979	-21.8838
14	0.3918	-0.1692	-0.4322	0.2272	0.0864	0.329	-0.0214	-0.1811	0.0583	0.7676	0.2072	0.0816	-0.8449	0.1314	0.1028	1.6597	-0.3888	0.0908	0.038	0.1813	0.2808	-4.728	10.826	-9.2829
15	0.0544	0.0481	-0.1256	0.061	-0.0882	0.1791	0.0533	-0.0811	-0.0592	-0.8022	-0.1845	-0.2275	0.5441	0.332	-0.0004	0.4679	0.0142	-0.0205	0.3549	0.0559	0.2931	-4.5408	-5.503	-20.504
16	1.1161	-0.3854	-0.4381	1.073	1.8428	3.4577	0.4208	-0.1889	0.4206	1.2494	0.3561	0.1806	-1.9245	0.657	0.7317	1.1062	-0.1784	0.1279	0.484	0.154	0.3628	-4.0104	5.4361	-0.7337
17	0.0835	0.1251	0.1016	0.073	0.0591	0.1012	0.169	0.1249	0.1134	0.4518	0.4574	0.9516	-0.3767	-0.2734	0.0115	0.5152	0.0207	0.0447	0.3383	0.0922	0.4336	-10.9477	4.3542	-12.8217
18	-0.0005	0.0115	-0.0027	0.0215	-0.0007	0.0117	0.3606	0.0533	0.0477	-0.2648	0.0609	0.2715	-0.141	-0.1142	-0	0.6	0.0098	-0.0318	0.394	0.0586	0.3371	-7.2135	5.7341	-28.7598
19	1.0444	0.1102	0.0925	0.0521	0.0696	0.4666	0.1334	0.315	-0.0531	0.4881	0.3093	1.1748	-0.0273	-0.4431	-0.0881	0.6937	0.1204	0.227	0.3447	0.2338	0.4821	-14.5182	3.1769	-8.5059
20	-0.03	0.126	0.0283	0.2437	-0.1572	0.0727	-0.0665	-0.2431	0.0584	0.8213	0.1075	0.8735	-0.4956	-0.4334	0.0003	0.4903	0.0146	0.0074	0.3954	0.0828	0.3845	-9.4808	-6.0972	-0.3789
21	0.1284	-0.1981	0.0999	0.5659	-0.2476	0.1191	0.455	0.3864	-0.058	-0.4909	-0.0709	0.4554	-0.2605	-0.4678	0.383	-0.1161	0.2457	-0.3111	0.7332	0.5648	0.9284	-20.2324	0.3328	-17.4072
22	0.6258	-0.2179	0.0003	1.0348	-0.244	0.1225	0.3737	-0.1505	0.1213	1.0355	-0.0356	0.3174	-0.4947	0.3917	0.2348	0.573	-0.2252	-0.0814	0.49	0.0444	0.3042	-2.0867	-3.1844	0.3654

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 31 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 32 through 41 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 42 through 52 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 53 through 65 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 66 through 73 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 74 through 80 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 81 through 92 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 93 through 104 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 105 through 125 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 126 through 134 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 2 through 12 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 13 through 31 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 32 through 39 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 40 through 52 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 53 through 65 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 66 through 73 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 74 through 80 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 81 through 92 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 93 through 104 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 105 through 115 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 116 through 134 )

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