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- PDB-9av6: Crystal structure of CMGC family protein kinase from Trichomonas ... -

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Basic information

Entry
Database: PDB / ID: 9av6
TitleCrystal structure of CMGC family protein kinase from Trichomonas vaginalis (Apo)
Componentsnon-specific serine/threonine protein kinase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / CMGC family protein kinase / Trichomonas vaginalis / HYDROLASE
Function / homology
Function and homology information


nuclear lumen / protein kinase CK2 complex / non-specific serine/threonine protein kinase / regulation of cell cycle / protein serine/threonine kinase activity / DNA damage response / regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol
Similarity search - Function
Casein Kinase 2, subunit alpha / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 CMGC family protein kinase from Trichomonas vaginalis (Apo)
Authors: Liu, L. / Lovell, S. / Cooper, A. / Battaile, K.P.
History
DepositionMar 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,51411
Polymers37,5531
Non-polymers96110
Water1,76598
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)88.374, 107.224, 42.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

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Components

#1: Protein non-specific serine/threonine protein kinase


Mass: 37553.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_125560 / Plasmid: TrvaA.01010.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A2F9N1, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: JCSG+ F2: 3.15 M Ammonium Sulfate, 0.1M Citrate, pH 5.0, TrvaA.01010.a.B1.PW39249 at 16.4 mg/mL. plate 13855 well F2 drop3. Puck: PSL-0906, Cryo: 2.5 M Lithium Sulfate.

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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: Feb 19, 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: 2→107.22 Å / Num. obs: 27825 / % possible obs: 100 % / Redundancy: 8.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.044 / Rrim(I) all: 0.128 / Χ2: 1.01 / Net I/σ(I): 9.3 / Num. measured all: 244482
Reflection shellResolution: 2→2.05 Å / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 1.165 / Num. measured all: 18096 / Num. unique obs: 1998 / CC1/2: 0.848 / Rpim(I) all: 0.41 / Rrim(I) all: 1.237 / Χ2: 1.08 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(dev_5250: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→68.2 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1413 5.1 %
Rwork0.1894 --
obs0.1913 27719 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→68.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 50 98 2654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112597
X-RAY DIFFRACTIONf_angle_d1.0243519
X-RAY DIFFRACTIONf_dihedral_angle_d12.462958
X-RAY DIFFRACTIONf_chiral_restr0.056388
X-RAY DIFFRACTIONf_plane_restr0.01438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.34231350.29042562X-RAY DIFFRACTION100
2.07-2.150.26851460.22672559X-RAY DIFFRACTION100
2.15-2.250.2671330.20172592X-RAY DIFFRACTION100
2.25-2.370.21551370.20942606X-RAY DIFFRACTION100
2.37-2.520.24351470.21582597X-RAY DIFFRACTION100
2.52-2.710.24331310.20012618X-RAY DIFFRACTION100
2.71-2.990.27771340.2162645X-RAY DIFFRACTION100
2.99-3.420.24151410.20282634X-RAY DIFFRACTION100
3.42-4.310.181620.1562664X-RAY DIFFRACTION100
4.31-68.20.22141470.17622829X-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)
10.7202-0.45110.03722.92121.04710.6297-0.15680.8180.0515-1.44180.0304-0.2623-0.75780.37190.09040.7091-0.06170.05910.6230.05810.54638.538210.2413-26.1154
23.1909-1.9545-0.15877.35081.14462.63920.15480.24110.3123-0.1907-0.479-0.5429-0.51810.3067-0.02020.26330.0012-0.05090.45840.05570.420121.33358.5314-10.6095
31.8904-0.08450.32715.9547-0.4411.5153-0.10190.10540.143-0.07560.0513-0.03820.08010.12950.08160.25330.0253-0.00370.3306-0.00760.27310.70023.0808-12.7922
41.4946-1.9495-0.40296.16120.9911.0227-0.12160.01090.03950.67730.0905-0.40140.11390.06290.00490.2870.035-0.03290.3098-0.00070.257517.6403-21.2755-7.691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 96 )
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 316 )

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