[English] 日本語
Yorodumi
- PDB-4yed: TcdA (CsdL) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yed
TitleTcdA (CsdL)
ComponentstRNA threonylcarbamoyladenosine dehydratase
KeywordsLIGASE / N6-threonylcarbamoyladenosine dehydratase tRNA modification
Function / homology
Function and homology information


Ligases; Forming carbon-oxygen bonds / tRNA threonylcarbamoyladenosine dehydratase / cyclic threonylcarbamoyladenosine biosynthetic process / ubiquitin-like modifier activating enzyme activity / sodium ion binding / potassium ion binding / protein homodimerization activity / ATP binding / membrane
Similarity search - Function
ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / tRNA threonylcarbamoyladenosine dehydratase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsKim, S. / Park, S.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
NRF2013R1A1A2005276 Korea, Republic Of
CitationJournal: J.Mol.Biol. / Year: 2015
Title: The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N(6)-Threonylcarbamoyladenosine Dehydratase Activity
Authors: Kim, S. / Lee, H. / Park, S.Y.
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA threonylcarbamoyladenosine dehydratase
B: tRNA threonylcarbamoyladenosine dehydratase
C: tRNA threonylcarbamoyladenosine dehydratase
D: tRNA threonylcarbamoyladenosine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,95912
Polymers117,2014
Non-polymers1,7578
Water10,323573
1
A: tRNA threonylcarbamoyladenosine dehydratase
B: tRNA threonylcarbamoyladenosine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4796
Polymers58,6012
Non-polymers8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-25 kcal/mol
Surface area19230 Å2
MethodPISA
2
C: tRNA threonylcarbamoyladenosine dehydratase
D: tRNA threonylcarbamoyladenosine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4796
Polymers58,6012
Non-polymers8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-27 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.555, 97.117, 83.337
Angle α, β, γ (deg.)90.00, 111.65, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
tRNA threonylcarbamoyladenosine dehydratase / t(6)A37 dehydratase


Mass: 29300.357 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 / Gene: tcdA, csdL, ygdL, b2812, JW2783 / Production host: Escherichia coli (E. coli)
References: UniProt: Q46927, Ligases; Forming carbon-oxygen bonds
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG 3350 and 0.15 M DL-malic acid, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 76402 / % possible obs: 100 % / Redundancy: 3.8 % / Net I/σ(I): 26.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.9→32.766 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.248 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20023 3837 5 %RANDOM
Rwork0.15931 ---
obs0.16138 72504 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.049 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å2-0.04 Å2
2--0.06 Å2-0 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7531 0 116 573 8220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197753
X-RAY DIFFRACTIONr_bond_other_d0.0010.027617
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.9810500
X-RAY DIFFRACTIONr_angle_other_deg0.897317420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.60723.531303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.001151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.361560
X-RAY DIFFRACTIONr_chiral_restr0.1120.21246
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021728
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5012.6814014
X-RAY DIFFRACTIONr_mcbond_other2.4992.684013
X-RAY DIFFRACTIONr_mcangle_it3.5713.9935000
X-RAY DIFFRACTIONr_mcangle_other3.5713.9945001
X-RAY DIFFRACTIONr_scbond_it3.8713.1873739
X-RAY DIFFRACTIONr_scbond_other3.873.1873739
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7124.5765501
X-RAY DIFFRACTIONr_long_range_B_refined7.40822.8529190
X-RAY DIFFRACTIONr_long_range_B_other7.28522.5598923
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 276 -
Rwork0.225 5263 -
obs--97.91 %

+
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