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- PDB-9zk0: Crystal structure of a calcium bound C2 domain containing protein... -

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Basic information

Entry
Database: PDB / ID: 9zk0
TitleCrystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis
ComponentsC2 domain containing protein
KeywordsLIPID BINDING PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / C2 domain
Function / homology
Function and homology information


calcium ion binding / membrane
Similarity search - Function
Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / C2 domain containing protein
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis
Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Buchko, G.W.
History
DepositionDec 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C2 domain containing protein
B: C2 domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4029
Polymers32,7662
Non-polymers6367
Water4,936274
1
A: C2 domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6573
Polymers16,3831
Non-polymers2742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C2 domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7466
Polymers16,3831
Non-polymers3635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.329, 50.197, 56.300
Angle α, β, γ (deg.)74.23, 82.17, 79.99
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 281 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 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. plate 20301 A9 drop 1, Puck: PSL-0103, Cryo: 20% PEG200 + 80% crystallant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 20, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.4→47.81 Å / Num. obs: 47847 / % possible obs: 92.9 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Χ2: 0.45 / Net I/σ(I): 8.4 / Num. measured all: 169832
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 64.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.438 / Num. measured all: 5415 / Num. unique obs: 1606 / CC1/2: 0.798 / Rpim(I) all: 0.28 / Rrim(I) all: 0.522 / Χ2: 0.44 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(2.0_5896: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→47.81 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 16.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1699 2370 4.95 %
Rwork0.1404 --
obs0.1419 47838 92.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2159 0 37 274 2470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082269
X-RAY DIFFRACTIONf_angle_d0.9843077
X-RAY DIFFRACTIONf_dihedral_angle_d15.233863
X-RAY DIFFRACTIONf_chiral_restr0.084354
X-RAY DIFFRACTIONf_plane_restr0.009386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.25871070.19631854X-RAY DIFFRACTION66
1.43-1.460.23431200.16992464X-RAY DIFFRACTION86
1.46-1.490.18821290.1412685X-RAY DIFFRACTION91
1.49-1.530.20311370.12822694X-RAY DIFFRACTION94
1.53-1.570.19811440.12652751X-RAY DIFFRACTION95
1.57-1.620.18031440.13162734X-RAY DIFFRACTION95
1.62-1.670.18661590.13242725X-RAY DIFFRACTION95
1.67-1.730.19741280.13232733X-RAY DIFFRACTION95
1.73-1.80.16371600.12342770X-RAY DIFFRACTION95
1.8-1.880.17731520.12722692X-RAY DIFFRACTION95
1.88-1.980.14731190.13042775X-RAY DIFFRACTION96
1.98-2.110.16771610.13282769X-RAY DIFFRACTION96
2.11-2.270.17451590.12882743X-RAY DIFFRACTION96
2.27-2.50.16141350.13632811X-RAY DIFFRACTION97
2.5-2.860.18811340.14822768X-RAY DIFFRACTION96
2.86-3.60.15031400.14842772X-RAY DIFFRACTION96
3.6-47.810.1561420.15042728X-RAY DIFFRACTION95

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