[English] 日本語
Yorodumi
- PDB-7vnx: Crystal structure of TkArkI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vnx
TitleCrystal structure of TkArkI
ComponentsTkArkI
KeywordsRNA BINDING PROTEIN / Kinase
Function / homology: / Protein kinase-like domain superfamily / GUANOSINE / Serine/threonine protein kinase
Function and homology information
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsYamashita, S. / Minowa, K. / Ohira, T. / Suzuki, T. / Tomita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H03980 Japan
CitationJournal: Nature / Year: 2022
Title: Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance.
Authors: Ohira, T. / Minowa, K. / Sugiyama, K. / Yamashita, S. / Sakaguchi, Y. / Miyauchi, K. / Noguchi, R. / Kaneko, A. / Orita, I. / Fukui, T. / Tomita, K. / Suzuki, T.
History
DepositionOct 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed
Revision 1.2May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TkArkI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2802
Polymers24,9971
Non-polymers2831
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint1 kcal/mol
Surface area10670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.850, 66.850, 98.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein TkArkI


Mass: 24996.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5JDQ4
#2: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→37.464 Å / Num. obs: 23021 / % possible obs: 100 % / Redundancy: 39.595 % / Biso Wilson estimate: 34.36 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.07 / Χ2: 0.87 / Net I/σ(I): 35.18 / Num. measured all: 911513 / Scaling rejects: 39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.8540.1791.9352.5567622168716830.8571.95999.8
1.85-1.941.3831.3983.7369110167016700.9291.416100
1.9-1.9540.9321.0315.165246159415940.9611.044100
1.95-2.0139.7180.7357.0362317156915690.9740.744100
2.01-2.0839.1740.5349.560015153215320.9880.541100
2.08-2.1541.1680.41112.6360146146214610.9910.41699.9
2.15-2.2341.9360.28817.8559297141414140.9970.291100
2.23-2.3341.2650.22622.4456161136113610.9970.229100
2.33-2.4339.5510.19325.7551100129212920.9980.196100
2.43-2.5539.2770.15131.3549175125212520.9990.152100
2.55-2.6941.5490.12539.0249776119811980.9990.127100
2.69-2.8541.1150.09948.546131112211220.9990.1100
2.85-3.0439.1820.07262.24418461068106810.073100
3.04-3.2936.5750.05971.953569797697610.06100
3.29-3.636.9720.04688.343390391791710.047100
3.6-4.0337.2260.04298.913030281481410.042100
4.03-4.6534.4330.038102.542537773773710.038100
4.65-5.735.5330.036103.462178261361310.036100
5.7-8.0635.6690.034105.091715748148110.034100
8.06-37.46435.030.029112.59935326926710.02999.3

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12-2829_1309refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.801→37.464 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 1151 5 %
Rwork0.1711 21863 -
obs0.1727 23014 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.27 Å2 / Biso mean: 42.5358 Å2 / Biso min: 24.04 Å2
Refinement stepCycle: final / Resolution: 1.801→37.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 20 77 1798
Biso mean--53.32 47.48 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121753
X-RAY DIFFRACTIONf_angle_d1.1232355
X-RAY DIFFRACTIONf_chiral_restr0.077262
X-RAY DIFFRACTIONf_plane_restr0.008301
X-RAY DIFFRACTIONf_dihedral_angle_d19.989670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.8012-1.88320.29021420.23012698
1.8832-1.98240.26231440.19712737
1.9824-2.10660.23921430.17882731
2.1066-2.26930.18231440.1632722
2.2693-2.49760.21281430.17382724
2.4976-2.85890.24781440.18762732
2.8589-3.60140.20311450.17782755
3.6014-37.4640.1811460.15652764
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)
18.8954-3.49084.70983.0964-2.24439.2220.16880.30230.5593-0.2688-0.3535-0.12330.10780.20310.17820.40130.01730.01680.27930.01270.306133.945919.2116-20.6287
23.2043-1.4239-3.03042.58462.06853.6437-0.0836-0.06630.0038-0.01990.0491-0.06680.07180.13530.04180.29860.0166-0.03420.2937-0.00770.30824.757423.5236-11.2508
32.60670.17910.69815.0465-0.70762.4099-0.050.2210.07550.0041-0.0132-0.0733-0.11610.24910.06840.24280.02040.00640.32080.03820.271420.930841.0993-0.1341
48.07441.6883-0.45695.8417-3.19967.6355-0.1336-0.88660.61950.8370.09090.1062-0.97960.03660.07090.40750.08060.02470.4421-0.08240.318514.693148.77411.9378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:23)A1 - 23
2X-RAY DIFFRACTION2(chain A and resid 24:99)A24 - 99
3X-RAY DIFFRACTION3(chain A and resid 100:185)A100 - 185
4X-RAY DIFFRACTION4(chain A and resid 186:216)A186 - 216

+
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