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- PDB-4jin: X-ray crystal structure of Archaeoglobus fulgidus Rio1 bound to (... -

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Basic information

Entry
Database: PDB / ID: 4jin
TitleX-ray crystal structure of Archaeoglobus fulgidus Rio1 bound to (2E)-N-benzyl-2-cyano-3-(pyridine-4-yl)acrylamide (WP1086)
ComponentsRIO-type serine/threonine-protein kinase Rio1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein kinase / Ribosome Biogenesis / pre-40S / autophosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


hydrolase activity / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine 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 / RIO1 family / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-1L7 / RIO-type serine/threonine-protein kinase Rio1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsMielecki, M. / Krawiec, K. / Kiburu, I. / Grzelak, K. / Wlodzimierz, Z. / Kierdaszuk, B. / Kowa, K. / Fokt, I. / Szymanski, S. / Piotr, S. ...Mielecki, M. / Krawiec, K. / Kiburu, I. / Grzelak, K. / Wlodzimierz, Z. / Kierdaszuk, B. / Kowa, K. / Fokt, I. / Szymanski, S. / Piotr, S. / Szeja, W. / Priebe, W. / Lesyng, B. / LaRonde-LeBlanc, N.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Development of novel molecular probes of the Rio1 atypical protein kinase.
Authors: Mielecki, M. / Krawiec, K. / Kiburu, I. / Grzelak, K. / Zagorski, W. / Kierdaszuk, B. / Kowa, K. / Fokt, I. / Szymanski, S. / Swierk, P. / Szeja, W. / Priebe, W. / Lesyng, B. / Laronde-Leblanc, N.
History
DepositionMar 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Sep 20, 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: RIO-type serine/threonine-protein kinase Rio1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4012
Polymers30,1381
Non-polymers2631
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.553, 52.608, 63.654
Angle α, β, γ (deg.)90.00, 109.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30137.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF_1804, rio1 / Plasmid: pDEST527 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (TM) DE3 pLysS
References: UniProt: O28471, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-1L7 / (2E)-N-benzyl-2-cyano-3-(pyridin-4-yl)prop-2-enamide


Mass: 263.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13N3O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.1 M MgCl2, 20% PEG 3350, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.095→29.25 Å / Num. all: 15780 / % possible obs: 96.39 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 46.37 Å2 / Rsym value: 0.073 / Net I/σ(I): 19.8
Reflection shellResolution: 2.1→2.26 Å / Redundancy: 2.6 % / Rsym value: 0.329 / % possible all: 87.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZTF

1ztf


Resolution: 2.095→29.249 Å / SU ML: 0.27 / σ(F): 1.37 / Phase error: 28.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 755 4.96 %
Rwork0.1788 --
obs0.1817 15211 96.4 %
all-15780 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.5863 Å2-0 Å22.4565 Å2
2---7.0564 Å2-0 Å2
3---10.6427 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.095→29.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 20 87 2158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082110
X-RAY DIFFRACTIONf_angle_d1.0642836
X-RAY DIFFRACTIONf_dihedral_angle_d14.614812
X-RAY DIFFRACTIONf_chiral_restr0.07306
X-RAY DIFFRACTIONf_plane_restr0.004364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0953-2.2570.28381500.22462615X-RAY DIFFRACTION88
2.257-2.4840.29921380.21942832X-RAY DIFFRACTION95
2.484-2.84320.29821660.21452964X-RAY DIFFRACTION99
2.8432-3.58110.2931550.19952989X-RAY DIFFRACTION100
3.5811-29.25190.18791460.15173056X-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)
10.57680.2439-0.12390.5513-0.64380.7668-0.05430.0363-0.0778-0.17720.1484-0.09230.30710.120100.4169-0.0257-0.01770.3556-0.02540.41718.9476.1087-1.6973
20.21050.1322-0.05630.0782-0.02040.57460.23520.41630.16940.028-0.26150.4815-0.4654-0.95620.01390.48410.014-0.05840.6713-0.02180.5824-4.67129.10675.0502
32.53580.4874-0.90471.1697-0.00761.2509-0.1343-0.0002-0.07780.22210.0065-0.09840.10790.032600.3918-0.00620.00650.36280.00270.31738.0656-1.354815.1346
40.7082-0.2420.24620.39750.32570.5937-0.1926-0.1217-0.43040.32390.00610.40510.2195-0.130900.4897-0.01210.11630.44620.03150.5875-0.791-8.457619.9627
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 108 )
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 201 )
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 258 )

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