SAXSdb — 9zk4

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1. Protein Identity and Related Structures Protein Identity & Related Structures

C2 domain containing protein

Trichomonas vaginalis G3

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–135	Fragment：residues 1-135	MLI MALONATE ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；Grid salt screen D3: 1.90 M sodium malonate, pH 6.0. TrvaA.01422.c.B2.PB00149 at 20 mg/mL. plate 20302 D3 drop 1, Puck: PSL-0112, Cryo: 3.40 M sodium alonate, pH 6.0	Resolution 1.30 Å R-free 0.171
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–135	Fragment：residues 1-135	MLI MALONATE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；Grid salt screen D3: 1.90 M sodium malonate, pH 6.0. TrvaA.01422.c.B2.PB00149 at 20 mg/mL. plate 20302 D3 drop 1, Puck: PSL-0112, Cryo: 3.40 M sodium alonate, pH 6.0	Resolution 1.30 Å R-free 0.171

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZK4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9ZK0 Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–135（135 aa） Fragment：residues 1-135	Not recorded	1PE PENTAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；Proplex A9 : 0.2M NaCl, 0.1M MES, pH 6.0, 20% PEG2000 MME. TrvaA.01422.c.B2.PB00149 at 20 mg/mL. plate 20301 A9 drop 1, Puck: PSL-0103, Cryo: 20% PEG200 + 80% crystallant	Resolution 1.40 Å R-free 0.170
9ZK0 Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–135（135 aa） Fragment：residues 1-135	Not recorded	CL CHLORIDE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；Proplex A9 : 0.2M NaCl, 0.1M MES, pH 6.0, 20% PEG2000 MME. TrvaA.01422.c.B2.PB00149 at 20 mg/mL. plate 20301 A9 drop 1, Puck: PSL-0103, Cryo: 20% PEG200 + 80% crystallant	Resolution 1.40 Å R-free 0.170
9ZK1 Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (P21 form) Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–135（135 aa） Fragment：residues 1-135	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；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. plate 20301 A9 drop 2, Puck: PSL-0105, Cryo: 20% PEG200 + 80% crystallant	Resolution 1.51 Å R-free 0.214
9ZK1 Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (P21 form) Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–135（135 aa） Fragment：residues 1-135	Not recorded	CA CALCIUM ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；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. plate 20301 A9 drop 2, Puck: PSL-0105, Cryo: 20% PEG200 + 80% crystallant	Resolution 1.51 Å R-free 0.214
9ZK1 Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (P21 form) Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–135（135 aa） Fragment：residues 1-135	Not recorded	CA CALCIUM ION × 3 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；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. plate 20301 A9 drop 2, Puck: PSL-0105, Cryo: 20% PEG200 + 80% crystallant	Resolution 1.51 Å R-free 0.214
9ZK1 Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (P21 form) Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–135（135 aa） Fragment：residues 1-135	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；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. plate 20301 A9 drop 2, Puck: PSL-0105, Cryo: 20% PEG200 + 80% crystallant	Resolution 1.51 Å R-free 0.214
9ZK2 Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (orthorhombic P form) Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–135（135 aa） Fragment：residues 1-135	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；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	Resolution 1.53 Å R-free 0.256
9ZK2 Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (orthorhombic P form) Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–135（135 aa） Fragment：residues 1-135	Not recorded	CA CALCIUM ION × 2 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；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	Resolution 1.53 Å R-free 0.256
9ZK3 Crystal structure of a C2 domain containing protein from Trichomonas vaginalis Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–135（135 aa） Fragment：residues 1-135	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Proplex C11: 0.1M sodium cacodylate, pH 6.5, 25% PEG 4000. 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 C11 drop 1, Puck: PSL-0108, Cryo: 20% PEG200 + 80% crystallant	Resolution 1.35 Å R-free 0.170
9ZK3 Crystal structure of a C2 domain containing protein from Trichomonas vaginalis Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–135（135 aa） Fragment：residues 1-135	Not recorded	PGE TRIETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；Proplex C11: 0.1M sodium cacodylate, pH 6.5, 25% PEG 4000. 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 C11 drop 1, Puck: PSL-0108, Cryo: 20% PEG200 + 80% crystallant	Resolution 1.35 Å R-free 0.170
9ZK5 Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (P61 form) Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–135（135 aa） Fragment：residues 1-135	Not recorded	CA CALCIUM ION × 3 CL CHLORIDE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；Berkeley C3: 100 mM CaCl2, 20% PEG 3350. TrvaA.01422.c.B2.PB00149 at 20 mg/mL. plate 20299 C3 drop 1, Puck: PSL-0312, Cryo: 20% PEG200 + 80% crystallant	Resolution 1.54 Å R-free 0.196
9ZK6 Crystal structure of a C2 domain containing protein from Trichomonas vaginalis in complex with pyrophosphate Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–135（135 aa） Fragment：residues 1-135	Not recorded	PPV PYROPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；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	Resolution 1.70 Å R-free 0.231
9ZK6 Crystal structure of a C2 domain containing protein from Trichomonas vaginalis in complex with pyrophosphate Deposited 2025-12-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–135（135 aa） Fragment：residues 1-135	Not recorded	PPV PYROPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；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	Resolution 1.70 Å R-free 0.231

6 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A2EZR3_TRIV3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–143； UniProt 1–135 Author chain B； PDBConstruct 9–143； UniProt 1–135

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9zk4
Deposition date deposition_date	2025-12-05
最后修订 last_revision	2025-12-17
Structure title title	Crystal structure of a malonate bound C2 domain containing protein from Trichomonas vaginalis (P21 form)
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, C2 domain, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.82 Å
Radius of gyration Rg (electron density) rg_electron	20.91 Å
Forward intensity I(0) i0	15510800.00
Molecular weight molecular_weight	31126.0 kDa
Excluded volume excluded_volume	39606 Å³
Envelope volume envelope_volume	47589 Å³
Hydration-shell volume shell_volume	19391 Å³
Envelope diameter envelope_diameter	76.1 Å
Shell Rg shell_rg	26.91 Å
Envelope Rg envelope_rg	21.37 Å
Shape Rg shape_rg	20.88 Å
Total Rg total_rg	21.90 Å
Total atoms total_atoms	2194
Residues n_residues	272
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	72.3 Å
Rg (real space) rg_real	21.78 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	1.5510e+07
I(0) uncertainty (real space) i0_real_error	2.1570e+05
Rg (reciprocal space) rg_reciprocal	21.78 Å
I(0) (reciprocal space) i0_reciprocal	15510000.0000
Solution quality estimate total_estimate	0.8088
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.7 Å
Skewness Skewness skewness	0.257
Kurtosis Kurtosis kurtosis	-0.439
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3852000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	C2 domain containing protein
Molecular weight formula_weight	16382.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2521

MAHHHHHHMYQLHVRVVEAKELPKMDTFGKCDAFAILQLNSSRNIHRTKVIEKTYTPVWNEEFHIPLEDVTIDTLTVFLKDEDKGSSDDPISLIKIPINQFPLGEVVDKWYSLIPVKGVKKGGQIRLTIHIAPLGATPFQKTD

来源 Source

来源生物 organism	Trichomonas vaginalis G3
NCBI Class编号 ncbi_taxonomy_id	412133
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	249

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8. Citations (1)

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Unit-cell length a length_a	25.206 Å
Unit-cell length b length_b	82.360 Å
Unit-cell length c length_c	56.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	46.540 Å
R factor r_factor	0.1435
R_work r_work	0.1420
R_free r_free	0.1708

fit	/app/data/saxs_computation/zk/9zk4/9zk4.fit
pddf	/app/data/pr_computation/zk/9zk4/9zk4.pr.out
profile	/app/data/saxs_computation/zk/9zk4/9zk4.dat

Crystal structure of a malonate bound C2 domain containing protein from Trichomonas vaginalis (P21 form)

1. Protein Identity and Related Structures Protein Identity & Related Structures

C2 domain containing protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction