[English] 日本語
Yorodumi
- PDB-4jin: X-ray crystal structure of Archaeoglobus fulgidus Rio1 bound to (... -

+
Open data


ID or keywords:

Loading...

-
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


non-specific serine/threonine protein kinase / hydrolase activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more