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- PDB-1tqm: Crystal Structure of A. fulgidus Rio2 Serine Protein Kinase Bound... -

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Basic information

Entry
Database: PDB / ID: 1tqm
TitleCrystal Structure of A. fulgidus Rio2 Serine Protein Kinase Bound to AMPPNP
Componentsconserved hypothetical protein
KeywordsRIBOSOME / SERINE KINASE / AMPPNP / ANP
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding
Similarity search - Function
RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO kinase / RIO-like kinase / RIO1 family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Tyrosine-protein kinase, active site / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Transferase(Phosphotransferase) domain 1 ...RIO2 kinase winged helix domain, N-terminal / Rio2, N-terminal / RIO kinase / RIO-like kinase / RIO1 family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Tyrosine-protein kinase, active site / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Winged helix-like DNA-binding domain superfamily / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RIO-type serine/threonine-protein kinase Rio2
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLaRonde-LeBlanc, N. / Wlodawer, A.
CitationJournal: Structure / Year: 2004
Title: Crystal Structure of A. fulgidus Rio2 Defines a New Family of Serine Protein Kinases
Authors: LaRonde-LeBlanc, N. / Wlodawer, A.
History
DepositionJun 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3642
Polymers32,8581
Non-polymers5061
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.165, 44.259, 62.097
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-332-

HOH

21A-451-

HOH

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Components

#1: Protein conserved hypothetical protein / Rio2


Mass: 32857.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: RIO2 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-pLysS / References: UniProt: O30245
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


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


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.57 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.83
Details: PEG 900, SODIUM PHOSPHATE, SODIUM CITRATE, pH 3.83, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99998 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 21, 2003
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.99→29 Å / Num. all: 21420 / Num. obs: 20313 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rsym value: 0.042 / Net I/σ(I): 40.9
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 12.1 / Rsym value: 0.125 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1tqi
Resolution: 1.99→28.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.353 / SU ML: 0.097 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22775 1106 5.2 %RANDOM
Rwork0.17134 ---
obs0.17435 20313 97.9 %-
all-21420 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.04 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.166 Å
Refinement stepCycle: LAST / Resolution: 1.99→28.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 31 197 2413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0212260
X-RAY DIFFRACTIONr_bond_other_d0.0020.022053
X-RAY DIFFRACTIONr_angle_refined_deg2.0671.9623053
X-RAY DIFFRACTIONr_angle_other_deg1.02334747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2875266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1580.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022486
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02487
X-RAY DIFFRACTIONr_nbd_refined0.2220.2503
X-RAY DIFFRACTIONr_nbd_other0.2550.22318
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.21295
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4661.51330
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.63722136
X-RAY DIFFRACTIONr_scbond_it4.0323930
X-RAY DIFFRACTIONr_scangle_it6.5524.5917
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
Rfree0.285 90 -
Rwork0.182 1347 -
obs--95.7 %

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