[English] 日本語
Yorodumi
- PDB-6agg: Crystal structure of agmatine-AMPPCP-Mg complexed TiaS (tRNAIle2 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6agg
TitleCrystal structure of agmatine-AMPPCP-Mg complexed TiaS (tRNAIle2 agmatidine synthetase)
ComponentstRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
KeywordsLIGASE / zinc ribbon / conformational change / TiaS / tRNA modification / Zinc finger engineering
Function / homology
Function and homology information


tRNAIle2-agmatinylcytidine synthase / ligase activity, forming carbon-nitrogen bonds / tRNA wobble cytosine modification / nucleic acid binding / ATP binding / cytoplasm
Similarity search - Function
Domain of unknown function DUF1743 / tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS / Domain of unknown function (DUF1743) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ACETATE ION / AGMATINE / AMMONIUM ION / tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.706 Å
AuthorsDong, J.S. / Gong, W.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)91219202 China
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structure of tRNA-Modifying Enzyme TiaS and Motions of Its Substrate Binding Zinc Ribbon.
Authors: Dong, J. / Li, F. / Gao, F. / Wei, J. / Lin, Y. / Zhang, Y. / Lou, J. / Liu, G. / Dong, Y. / Liu, L. / Liu, H. / Wang, J. / Gong, W.
History
DepositionAug 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
Z: tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2589
Polymers48,3721
Non-polymers8868
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-25 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.786, 69.786, 210.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 1 molecules Z

#1: Protein tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS / tRNA(Ile2)-agm2C synthetase / tRNA(Ile2) agmatidine synthetase


Mass: 48372.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: tiaS, AF_2259 / Production host: Escherichia coli (E. coli)
References: UniProt: O28025, tRNAIle2-agmatinylcytidine synthase

-
Non-polymers , 7 types, 16 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-AG2 / AGMATINE / (4-AMINOBUTYL)GUANIDINE


Mass: 130.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14N4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50mM HEPES-Na pH7.0-7.2, 0.5M NH4Ac, 0.2M MgCl2, 1.5-2.5% PEG 8000
PH range: 6.7-7.2

-
Data collection

DiffractionMean temperature: 80 K / Ambient temp details: in liquid nitrogen stream
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 14875 / % possible obs: 99.3 % / Redundancy: 27.3 % / Rmerge(I) obs: 0.123 / Χ2: 1.5 / Net I/σ(I): 24.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 28.6 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 11 / Num. unique obs: 1461 / Χ2: 1.73 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.706→29.095 Å / SU ML: 0.76 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.62
RfactorNum. reflection% reflectionSelection details
Rfree0.2978 735 5.01 %Random selection per shell
Rwork0.2109 ---
obs0.215 14667 97.87 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 67.781 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.6712 Å20 Å2-0 Å2
2--16.6712 Å20 Å2
3----33.3425 Å2
Refinement stepCycle: LAST / Resolution: 2.706→29.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 52 8 3425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073486
X-RAY DIFFRACTIONf_angle_d1.0794713
X-RAY DIFFRACTIONf_dihedral_angle_d16.7061327
X-RAY DIFFRACTIONf_chiral_restr0.073513
X-RAY DIFFRACTIONf_plane_restr0.004613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7064-2.91520.42481530.31142660X-RAY DIFFRACTION96
2.9152-3.20820.31271530.22062729X-RAY DIFFRACTION99
3.2082-3.67170.32371390.21732782X-RAY DIFFRACTION99
3.6717-4.62290.29331520.19772787X-RAY DIFFRACTION98
4.6229-29.09640.27041380.20132974X-RAY DIFFRACTION98
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)
14.0372.05211.39054.6433-0.53816.72620.2430.3075-0.082-0.82480.28630.6936-0.3254-0.0319-0.38270.76130.2019-0.06580.340.04050.57728.934813.099233.5623
21.94152.28490.28434.92880.17195.3291-0.5271.18130.4973-0.02460.1098-0.8943-0.57610.39530.30890.68810.1460.19090.51390.05680.368311.06126.621538.512
32.68731.9206-0.62775.6634-1.0537.4287-0.0420.0588-0.4176-0.27670.12460.0231-0.0127-0.5229-0.1890.59830.15460.05540.36230.03170.55376.7991.415834.8482
42.63793.24831.71395.273-0.26775.5135-0.0938-0.24410.0063-0.25070.45760.1998-0.0313-0.1468-0.13830.50890.1063-0.01310.42150.01450.57268.11294.665439.2232
54.6374-0.29890.50683.45390.32835.5768-0.3624-0.32820.89880.42470.0239-0.3463-1.66551.43550.21581.1064-0.2559-0.11950.63490.00430.57924.881823.914842.6789
63.75640.2698-0.03261.02180.74834.22210.2155-0.4435-0.6001-0.005-0.12650.5325-0.01120.1734-0.050.48180.15510.07020.36790.04750.490216.08692.453652.2419
70.58250.17480.10352.04040.38542.41160.1862-1.1358-0.49560.1892-0.2832-0.86650.25571.2042-0.09130.41750.2452-0.12811.02070.50040.66532.5332-1.79761.1095
82.2140.42641.56230.07350.29811.08590.2419-0.54330.05630.37160.5070.03040.2496-0.3613-0.8680.68080.2452-0.10921.17670.17830.722536.58551.030173.1399
94.4025-0.11772.50514.3025-0.21085.8146-0.0816-1.3578-0.1809-0.37770.0803-1.09660.2505-0.8108-0.28621.04580.0677-0.05021.1841-0.03680.841957.07481.849192.1384
101.8811-0.53222.31831.6662-1.65813.9095-0.1332-0.58420.00830.38480.0293-0.1703-0.89770.8642-0.01160.9652-0.0892-0.0661.0630.05950.598927.36312.008362.6605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'Z' and (resseq 1:44)
2X-RAY DIFFRACTION2chain 'Z' and (resseq 45:67)
3X-RAY DIFFRACTION3chain 'Z' and (resseq 68:128)
4X-RAY DIFFRACTION4chain 'Z' and (resseq 129:162)
5X-RAY DIFFRACTION5chain 'Z' and (resseq 163:238)
6X-RAY DIFFRACTION6chain 'Z' and (resseq 239:264)
7X-RAY DIFFRACTION7chain 'Z' and (resseq 265:327)
8X-RAY DIFFRACTION8chain 'Z' and (resseq 328:353)
9X-RAY DIFFRACTION9chain 'Z' and (resseq 354:384)
10X-RAY DIFFRACTION10chain 'Z' and (resseq 385:420)

+
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://pdbjlvh1.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