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- PDB-9zk4: Crystal structure of a malonate bound C2 domain containing protei... -

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Basic information

Entry
Database: PDB / ID: 9zk4
TitleCrystal structure of a malonate bound C2 domain containing protein from Trichomonas vaginalis (P21 form)
ComponentsC2 domain containing protein
KeywordsLIPID BINDING PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / C2 domain
Function / homologyProtein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / calcium ion binding / membrane / MALONATE ION / C2 domain containing protein
Function and homology information
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 malonate bound C2 domain containing protein from Trichomonas vaginalis (P21 form)
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

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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)33,0647
Polymers32,7662
Non-polymers2985
Water4,486249
1
A: C2 domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5564
Polymers16,3831
Non-polymers1733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C2 domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5083
Polymers16,3831
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.206, 82.360, 56.780
Angle α, β, γ (deg.)90.00, 96.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
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: 1.79 Å3/Da / Density % sol: 31.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 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

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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: 1.3→46.54 Å / Num. obs: 54463 / % possible obs: 96.3 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Χ2: 0.99 / Net I/σ(I): 13.2 / Num. measured all: 355779
Reflection shellResolution: 1.3→1.32 Å / % possible obs: 66.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.306 / Num. measured all: 9046 / Num. unique obs: 1895 / CC1/2: 0.925 / Rpim(I) all: 0.154 / Rrim(I) all: 0.345 / Χ2: 0.9 / Net I/σ(I) obs: 4

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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: 1.3→46.54 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1708 2709 4.98 %
Rwork0.142 --
obs0.1435 54412 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 17 249 2443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052332
X-RAY DIFFRACTIONf_angle_d0.8373183
X-RAY DIFFRACTIONf_dihedral_angle_d17.072897
X-RAY DIFFRACTIONf_chiral_restr0.078367
X-RAY DIFFRACTIONf_plane_restr0.007406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.22381120.15891903X-RAY DIFFRACTION67
1.32-1.350.18151220.14922113X-RAY DIFFRACTION76
1.35-1.380.18251110.13552533X-RAY DIFFRACTION90
1.38-1.410.20921340.13292837X-RAY DIFFRACTION100
1.41-1.440.18131370.13282776X-RAY DIFFRACTION100
1.44-1.480.18551410.13212861X-RAY DIFFRACTION100
1.48-1.520.17561750.13172778X-RAY DIFFRACTION100
1.52-1.560.18071390.13122848X-RAY DIFFRACTION100
1.56-1.610.15821400.1282809X-RAY DIFFRACTION100
1.61-1.670.1831520.12612840X-RAY DIFFRACTION100
1.67-1.730.16191360.13412766X-RAY DIFFRACTION100
1.73-1.810.17361390.13592869X-RAY DIFFRACTION100
1.81-1.910.15921660.13042788X-RAY DIFFRACTION100
1.91-2.030.16751230.13092838X-RAY DIFFRACTION100
2.03-2.190.15721360.13232839X-RAY DIFFRACTION100
2.19-2.40.19791680.14082799X-RAY DIFFRACTION100
2.41-2.750.16681540.15342825X-RAY DIFFRACTION100
2.75-3.470.16951570.1532823X-RAY DIFFRACTION100
3.47-46.540.15891670.15262858X-RAY DIFFRACTION100

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