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- PDB-9zk5: Crystal structure of a calcium bound C2 domain containing protein... -

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Basic information

Entry
Database: PDB / ID: 9zk5
TitleCrystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (P61 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 / C2 domain containing protein
Function and homology information
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 (P61 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9638
Polymers16,3831
Non-polymers5807
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.280, 72.280, 76.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein C2 domain containing protein


Mass: 16382.914 Da / Num. of mol.: 1 / 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.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 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

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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: 1.54→48.36 Å / Num. obs: 33479 / % possible obs: 100 % / Redundancy: 20.6 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.015 / Rrim(I) all: 0.067 / Χ2: 1.06 / Net I/σ(I): 23.5 / Num. measured all: 690569
Reflection shellResolution: 1.54→1.58 Å / % possible obs: 100 % / Redundancy: 21.1 % / Rmerge(I) obs: 1.913 / Num. measured all: 51663 / Num. unique obs: 2452 / CC1/2: 0.822 / Rpim(I) all: 0.427 / Rrim(I) all: 1.96 / Χ2: 0.89 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5765: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→36.14 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 1696 5.07 %
Rwork0.1731 --
obs0.1741 33421 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→36.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 31 187 1330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091163
X-RAY DIFFRACTIONf_angle_d0.9681569
X-RAY DIFFRACTIONf_dihedral_angle_d14.019446
X-RAY DIFFRACTIONf_chiral_restr0.065178
X-RAY DIFFRACTIONf_plane_restr0.008196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.590.30841540.2772619X-RAY DIFFRACTION100
1.59-1.640.27031160.23762664X-RAY DIFFRACTION100
1.64-1.70.24441550.22712600X-RAY DIFFRACTION100
1.7-1.760.24931720.24052622X-RAY DIFFRACTION100
1.76-1.840.27121380.20822633X-RAY DIFFRACTION100
1.84-1.940.19331250.16722645X-RAY DIFFRACTION100
1.94-2.060.18571490.17282645X-RAY DIFFRACTION100
2.06-2.220.17791370.16552624X-RAY DIFFRACTION100
2.22-2.440.19121380.17562667X-RAY DIFFRACTION100
2.44-2.80.18781560.18382613X-RAY DIFFRACTION100
2.8-3.520.21321250.17792679X-RAY DIFFRACTION100
3.53-36.140.16921310.15042714X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.68840.3824-0.00850.90050.18740.7395-0.19650.2831-0.2376-0.29770.10430.05730.6421-0.34790.1090.569-0.06340.03010.3265-0.03930.3346-26.1479-15.2099-4.7886
20.46620.16670.47671.0339-0.52120.9153-0.112-0.1086-0.01230.11340.1305-0.0310.01720.0176-00.29310.01350.02190.2393-0.01140.2411-26.24984.82728.5125
30.11720.0468-0.0570.0238-0.02110.02220.16550.78490.2081-0.5915-0.0969-0.11660.1404-0.1333-00.52870.01470.10250.4599-0.01630.309-20.6893-2.5919-8.5286
40.3396-0.0004-0.2860.1829-0.08050.2696-0.0485-0.04860.0695-0.01370.1820.5621-0.1586-0.5065-00.28620.00880.01180.31330.0440.3225-33.76371.657.0992
50.06260.04240.00880.4658-0.2140.58810.23950.5982-0.021-0.7744-0.12190.0040.2660.0424-0.00290.56170.03130.01680.3813-0.0860.3859-22.4661-12.7456-7.058
60.39020.3968-0.29750.3878-0.29080.2129-0.01030.01070.0383-0.20620.09660.0559-0.0018-0.0618-00.3104-00.03050.27940.00510.2949-23.53895.19292.7336
70.4502-0.14970.53390.1117-0.15920.6157-0.00660.1339-0.0291-0.28360.1797-0.4710.12630.128400.3399-0.00350.05740.2771-0.04530.3821-18.0377-6.86233.9401
81.73340.1480.07020.02130.05750.5023-0.0154-0.3848-0.3611-0.05680.01730.32510.3674-0.16280.09520.3589-0.0167-0.02350.19570.02610.3171-25.5853-17.2725.0826
90.0998-0.0396-0.0030.02650.02960.1929-0.0957-0.1720.06820.46460.1195-0.5829-0.21280.25100.3458-0.0256-0.03850.3175-0.02610.3976-17.35471.807712.979
101.2199-0.61350.5111.2462-0.7070.41550.06220.0233-0.3325-0.6475-0.01320.4310.1498-0.3210.10680.4474-0.0802-0.07610.2575-0.01950.3815-30.3916-18.1641-1.9199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 39 )
4X-RAY DIFFRACTION4chain 'A' and (resid 40 through 52 )
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 65 )
6X-RAY DIFFRACTION6chain 'A' and (resid 66 through 80 )
7X-RAY DIFFRACTION7chain 'A' and (resid 81 through 92 )
8X-RAY DIFFRACTION8chain 'A' and (resid 93 through 104 )
9X-RAY DIFFRACTION9chain 'A' and (resid 105 through 115 )
10X-RAY DIFFRACTION10chain 'A' and (resid 116 through 135 )

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