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- PDB-9bkw: Crystal structure of a C2 domain from Trichomonas vaginalis -

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Basic information

Entry
Database: PDB / ID: 9bkw
TitleCrystal structure of a C2 domain from Trichomonas vaginalis
ComponentsXYPPX repeat family protein
KeywordsLIPID BINDING PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Trichomonas vaginalis / C2 domain
Function / homologyC2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / calcium ion binding / XYPPX repeat family protein
Function and homology information
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle 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 C2 domain from Trichomonas vaginalis
Authors: Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P.
History
DepositionApr 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XYPPX repeat family protein


Theoretical massNumber of molelcules
Total (without water)15,9051
Polymers15,9051
Non-polymers00
Water90150
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)81.657, 81.657, 41.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

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Components

#1: Protein XYPPX repeat family protein


Mass: 15905.209 Da / Num. of mol.: 1 / Fragment: M1-E130
Source method: isolated from a genetically manipulated source
Details: C2 domain / Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_347440 / Plasmid: TrvaA.17083.b.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2FNQ6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Grid Screen Salt HT C10: 2.4 M Sodium malonate pH 5.0, TrvaA.17083.b.B2.PB00135 at 12 mg/mL. plate 13979 well C10 drop 1, Puck: PSL-0101, Cryo: 3.0M Malonate, pH 7.0.

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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: Apr 13, 2024
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: 1.85→41.46 Å / Num. obs: 12504 / % possible obs: 100 % / Redundancy: 25.6 % / CC1/2: 0.999 / Rpim(I) all: 0.039 / Rrim(I) all: 0.199 / Rsym value: 0.195 / Net I/σ(I): 14.8
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 24.8 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 900 / CC1/2: 0.68 / Rpim(I) all: 0.483 / Rrim(I) all: 2.422 / Rsym value: 2.372 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40.83 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 637 5.11 %
Rwork0.1923 --
obs0.1939 12462 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 0 50 1087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121070
X-RAY DIFFRACTIONf_angle_d1.1151459
X-RAY DIFFRACTIONf_dihedral_angle_d14.661379
X-RAY DIFFRACTIONf_chiral_restr0.073163
X-RAY DIFFRACTIONf_plane_restr0.008186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.990.24511350.2282310X-RAY DIFFRACTION100
1.99-2.190.24391260.18882306X-RAY DIFFRACTION100
2.19-2.510.23041250.19742329X-RAY DIFFRACTION100
2.51-3.160.25281310.21172368X-RAY DIFFRACTION100
3.16-40.830.20451200.17912512X-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)
11.4026-0.8669-0.35331.049-0.3680.38490.03970.14380.0361-0.1836-0.02080.01-0.05570.17290.00150.22330.01750.02830.1590.01850.162310.782726.20812.8038
21.61040.1780.80651.7474-1.30071.45850.17010.21460.2919-0.2043-0.0911-0.11970.06380.01850.00730.1680.00440.02340.18350.00640.193310.482829.61490.1124
31.45980.1496-0.24061.19821.20371.52810.0545-0.05820.07280.1016-0.03350.0592-0.0466-0.1957-00.21750.00660.02670.17160.00950.21366.412629.06668.1521
41.5068-0.7273-1.16911.01620.45970.822-0.03180.0999-0.35610.18850.02030.23370.22960.1223-0.00050.21190.01520.02060.11220.00640.21517.669919.78016.4332
50.0141-0.0221-0.01440.01190.04980.06830.3531-0.0013-0.67090.7822-0.0703-0.75850.0642-0.0156-0.00020.805-0.1125-0.03370.6318-0.04870.639322.484227.818619.1684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 95 )
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 123 )
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 129 )

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