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- PDB-3re4: Crystal Structure of Archaeoglobus Fulgidus Rio1 Kinase bound to ... -

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Basic information

Entry
Database: PDB / ID: 3re4
TitleCrystal Structure of Archaeoglobus Fulgidus Rio1 Kinase bound to Toyocamycin.
ComponentsRIO-type serine/threonine-protein kinase Rio1
KeywordsTRANSFERASE/ANTIBIOTIC / Atypical Kinase / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity ...3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / hydrolase activity / protein serine kinase activity / ATP binding / metal ion binding
Similarity search - Function
: / RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / : / RIO domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-TO1 / RIO-type serine/threonine-protein kinase Rio1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å
AuthorsKiburu, I.N. / LaRonde-LeBlanc, N.
CitationJournal: Plos One / Year: 2012
Title: Interaction of rio1 kinase with toyocamycin reveals a conformational switch that controls oligomeric state and catalytic activity.
Authors: Kiburu, I.N. / Laronde-Leblanc, N.
History
DepositionApr 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIO-type serine/threonine-protein kinase Rio1
B: RIO-type serine/threonine-protein kinase Rio1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8584
Polymers60,2752
Non-polymers5832
Water3,099172
1
A: RIO-type serine/threonine-protein kinase Rio1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4292
Polymers30,1381
Non-polymers2911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RIO-type serine/threonine-protein kinase Rio1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4292
Polymers30,1381
Non-polymers2911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.814, 72.607, 60.561
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 3:85 or resseq 93:102 or resseq 106:258 )
211chain B and (resseq 3:85 or resseq 93:102 or resseq 106:258 )

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Components

#1: Protein RIO-type serine/threonine-protein kinase Rio1 / AfRio1


Mass: 30137.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: rio1, AF_1804 / Plasmid: PDEST527 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: O28471, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-TO1 / 4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile / TOYOCAMYCIN


Mass: 291.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H13N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 1.93 Å3/Da / Density % sol: 36.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 24% PEG 3350, 0.2 M Mg (CH3COO)2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2009
RadiationMonochromator: KOHZU HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.997→34.943 Å / Num. all: 30275 / Num. obs: 30275 / % possible obs: 97.14 % / Observed criterion σ(F): 1.36 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.069 / Net I/σ(I): 5.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.997→34.943 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 1533 5.06 %
Rwork0.215 --
obs0.2173 30275 97.14 %
all-31031 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.598 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5059 Å20 Å2-4.1234 Å2
2--6.773 Å20 Å2
3----9.2789 Å2
Refinement stepCycle: LAST / Resolution: 1.997→34.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4107 0 42 172 4321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114225
X-RAY DIFFRACTIONf_angle_d1.3855676
X-RAY DIFFRACTIONf_dihedral_angle_d16.8161638
X-RAY DIFFRACTIONf_chiral_restr0.085611
X-RAY DIFFRACTIONf_plane_restr0.004720
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2014X-RAY DIFFRACTIONPOSITIONAL
12B2014X-RAY DIFFRACTIONPOSITIONAL0.059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.997-2.06160.29991250.242431X-RAY DIFFRACTION91
2.0616-2.13520.29051270.22192604X-RAY DIFFRACTION97
2.1352-2.22070.31351340.21512590X-RAY DIFFRACTION97
2.2207-2.32180.27161450.21372596X-RAY DIFFRACTION97
2.3218-2.44410.27941240.212627X-RAY DIFFRACTION97
2.4441-2.59720.27651350.22622629X-RAY DIFFRACTION98
2.5972-2.79770.30831520.22932622X-RAY DIFFRACTION98
2.7977-3.07910.29171530.2292630X-RAY DIFFRACTION98
3.0791-3.52430.26391370.22422644X-RAY DIFFRACTION98
3.5243-4.43880.21531370.19922678X-RAY DIFFRACTION99
4.4388-34.94850.22811640.20412691X-RAY DIFFRACTION98

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