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- PDB-1ztf: Crystal Structure of A.fulgidus Rio1 serine protein kinase -

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Basic information

Entry
Database: PDB / ID: 1ztf
TitleCrystal Structure of A.fulgidus Rio1 serine protein kinase
ComponentsRio1 serine protein kinase
KeywordsTRANSFERASE / protein Kinase / ribosome biogenesis / rRNA
Function / homology
Function and homology information


preribosome, small subunit precursor / maturation of SSU-rRNA / hydrolase activity / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
RIO kinase, conserved site / RIO1/ZK632.3/MJ0444 family signature. / RIO kinase / RIO-like kinase / RIO1 family / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-XYA / : / RIO-type serine/threonine-protein kinase Rio1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å
AuthorsWlodawer, A. / LaRonde-LeBlanc, N.
CitationJournal: Febs J. / Year: 2005
Title: Structure and activity of the atypical serine kinase Rio1.
Authors: Laronde-Leblanc, N. / Guszczynski, T. / Copeland, T. / Wlodawer, A.
History
DepositionMay 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rio1 serine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9212
Polymers30,6541
Non-polymers2671
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.987, 52.701, 63.779
Angle α, β, γ (deg.)90.00, 108.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rio1 serine protein kinase


Mass: 30653.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: Rio1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: GenBank: 11499392, UniProt: O28471*PLUS
#2: Chemical ChemComp-XYA / 2-(6-AMINO-OCTAHYDRO-PURIN-9-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL / 9-BETA-D-XYLOFURANOSYL-ADENINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.35 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.3
Details: PEG 4000, MES, ammonuim sulfate, pH 6.3, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9794, 0.9795, 1.0000
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 6, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97951
311
ReflectionResolution: 1.99→40 Å / Num. all: 18480 / Num. obs: 18215 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.066

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.99→39.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.15 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23569 948 5.1 %RANDOM
Rwork0.16304 ---
obs0.16683 17678 99.67 %-
all-18480 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.304 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.07 Å2
2---0.01 Å20 Å2
3----0.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.214 Å
Refinement stepCycle: LAST / Resolution: 1.99→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 19 249 2313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0222103
X-RAY DIFFRACTIONr_bond_other_d00.021934
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.9962829
X-RAY DIFFRACTIONr_angle_other_deg0.88534500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9795252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48424.34399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.89815398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4411513
X-RAY DIFFRACTIONr_chiral_restr0.1630.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022300
X-RAY DIFFRACTIONr_gen_planes_other00.02431
X-RAY DIFFRACTIONr_nbd_refined0.2680.3516
X-RAY DIFFRACTIONr_nbd_other0.2540.31958
X-RAY DIFFRACTIONr_nbtor_refined0.2060.51047
X-RAY DIFFRACTIONr_nbtor_other0.1030.51210
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.5264
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1170.52
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.311
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.351
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.527
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.14521318
X-RAY DIFFRACTIONr_mcbond_other2.6572517
X-RAY DIFFRACTIONr_mcangle_it9.21832017
X-RAY DIFFRACTIONr_scbond_it10.6712938
X-RAY DIFFRACTIONr_scangle_it13.0563812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 58 -
Rwork0.195 1270 -
obs--96.79 %

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