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- PDB-3q60: Crystal structure of virulent allele ROP5B pseudokinase domain bo... -

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Basic information

Entry
Database: PDB / ID: 3q60
TitleCrystal structure of virulent allele ROP5B pseudokinase domain bound to ATP
ComponentsROP5B
KeywordsTRANSFERASE / pseudokinase / toxoplasma / 551.m00238 / ROP5
Function / homology
Function and homology information


protein kinase activity / ATP binding / metal ion binding
Similarity search - Function
Rhoptry protein, Rop2-like / Protein kinase-like domain, Apicomplexa / Kinase-like / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain ...Rhoptry protein, Rop2-like / Protein kinase-like domain, Apicomplexa / Kinase-like / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / MALONATE ION / Rhoptry protein 5B
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsReese, M.L. / Boothroyd, J.C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: A conserved non-canonical motif in the pseudoactive site of the ROP5 pseudokinase domain mediates its effect on Toxoplasma virulence.
Authors: Reese, M.L. / Boothroyd, J.C.
History
DepositionDec 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ROP5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8765
Polymers41,2181
Non-polymers6584
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.358, 69.329, 43.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

21A-632-

HOH

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Components

#1: Protein ROP5B


Mass: 41218.145 Da / Num. of mol.: 1 / Fragment: Pseudokinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: ROP5B;TGGT1_042710 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: F2YGR7*PLUS, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGENOMIC SEQUENCE ENCODING THE PROTEIN HAS BEEN DEPOSITED IN GENBANK ACCESSION HQ916448.

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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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG-3350, 0.3M Sodium malonate, 0.02M MgCl2, 0.01M ATP, pH 5.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2010 / Details: Rh coated flat mirror
RadiationMonochromator: Si(111) Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 40071 / % possible obs: 98.8 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.072 / Χ2: 0.986 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.72-1.789.30.5435580.945189
1.78-1.8512.50.44139480.967199.3
1.85-1.9414.30.32139840.964199.9
1.94-2.0414.70.21940040.9591100
2.04-2.1714.80.15440270.9491100
2.17-2.3314.80.11640080.9631100
2.33-2.5714.70.09140601.0361100
2.57-2.9414.70.07140590.9171100
2.94-3.7114.50.06141221.0411100
3.71-5013.60.05343011.095199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→30.219 Å / Occupancy max: 1 / Occupancy min: 0.48 / SU ML: 0.18 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1958 5.01 %
Rwork0.1788 --
obs0.1804 39069 96.63 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.464 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso max: 84.31 Å2 / Biso mean: 30.6359 Å2 / Biso min: 12.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.0762 Å20 Å2-0 Å2
2--5.4884 Å2-0 Å2
3----4.4122 Å2
Refinement stepCycle: LAST / Resolution: 1.72→30.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 40 276 3049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172841
X-RAY DIFFRACTIONf_angle_d1.7073864
X-RAY DIFFRACTIONf_chiral_restr0.115443
X-RAY DIFFRACTIONf_plane_restr0.009492
X-RAY DIFFRACTIONf_dihedral_angle_d14.3521050
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.7810.33351650.26133049321481
1.781-1.85230.28861860.22373495368193
1.8523-1.93660.25591910.19423664385597
1.9366-2.03860.24311970.18483726392398
2.0386-2.16630.22361980.17953778397699
2.1663-2.33350.21111980.17373773397199
2.3335-2.56830.22122030.169938314034100
2.5683-2.93960.20552010.17138304031100
2.9396-3.70250.19212050.169639024107100
3.7025-30.22360.18942140.178440634277100

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