[English] 日本語
Yorodumi
- PDB-3re4: Crystal Structure of Archaeoglobus Fulgidus Rio1 Kinase bound to ... -

+
Open data


ID or keywords:

Loading...

-
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


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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 )

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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