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- PDB-9av7: Crystal structure of CMGC family protein kinase from Trichomonas ... -

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Basic information

Entry
Database: PDB / ID: 9av7
TitleCrystal structure of CMGC family protein kinase from Trichomonas vaginalis (AMP-PNP)
Componentsnon-specific serine/threonine protein kinase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / CMGC family protein kinase / Trichomonas vaginalis
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 (AMP-PNP)
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,0592
Polymers37,5531
Non-polymers5061
Water1,15364
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)87.554, 108.124, 41.554
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-564-

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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: JCSG+ B7: 0.10 M Sodium acetate, pH 4.6, 8.0% (w/v) PEG 4000, TrvaA.01010.a.B1.PW39249 at 16.4 mg/mL. 2mM AMP-PNP and 2mM MgCl2 added prior to crystallization. No Mg bound. plate 13860 well ...Details: JCSG+ B7: 0.10 M Sodium acetate, pH 4.6, 8.0% (w/v) PEG 4000, TrvaA.01010.a.B1.PW39249 at 16.4 mg/mL. 2mM AMP-PNP and 2mM MgCl2 added prior to crystallization. No Mg bound. plate 13860 well B7 drop 2. Puck: PSL-0807, Cryo: 25% PEG 200 + 75% 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: 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: 2.1→108.12 Å / Num. obs: 23781 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.039 / Rrim(I) all: 0.122 / Χ2: 1.05 / Net I/σ(I): 9.9 / Num. measured all: 235482
Reflection shellResolution: 2.1→2.15 Å / % possible obs: 99.8 % / Redundancy: 10.4 % / Rmerge(I) obs: 1.314 / Num. measured all: 17827 / Num. unique obs: 1713 / CC1/2: 0.816 / Rpim(I) all: 0.416 / Rrim(I) all: 1.381 / Χ2: 1.09 / 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: 2.1→54.06 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1127 4.75 %
Rwork0.1994 --
obs0.2017 23711 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→54.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 31 64 2502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092498
X-RAY DIFFRACTIONf_angle_d1.013393
X-RAY DIFFRACTIONf_dihedral_angle_d16.132952
X-RAY DIFFRACTIONf_chiral_restr0.051381
X-RAY DIFFRACTIONf_plane_restr0.009424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.20.31951520.30132769X-RAY DIFFRACTION100
2.2-2.310.24661150.24942787X-RAY DIFFRACTION99
2.31-2.460.27831550.23322747X-RAY DIFFRACTION100
2.46-2.650.31681500.24452759X-RAY DIFFRACTION100
2.65-2.910.29651240.2432821X-RAY DIFFRACTION100
2.91-3.330.28571260.22992842X-RAY DIFFRACTION100
3.33-4.20.23481500.1872862X-RAY DIFFRACTION100
4.2-54.060.20721550.16272997X-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)
16.8465-1.9027-0.42867.5994-1.25595.1026-0.1628-0.28120.06320.2013-0.1630.07720.06010.34430.290.29180.0142-0.03010.34460.02340.305114.2983-5.929112.5775
21.27391.2053-0.88157.34480.62630.90790.06130.0122-0.0916-1.0333-0.2297-0.5405-0.15330.21470.1820.38620.04150.02230.4567-0.01950.331716.01737.23785.564
32.70112.07341.21388.97742.93843.25260.1753-0.40240.221-0.1082-0.49370.0699-0.1944-0.12960.26260.3267-0.04020.00410.4187-0.0020.255118.169228.510114.8664
44.96081.51651.23873.84291.9732.8327-0.2550.94930.4134-2.09220.2221-0.3076-0.92160.06370.03331.1522-0.0480.02440.48540.07030.503818.405524.9816-2.5104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 176 )
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 273 )
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 318 )

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