[English] 日本語
Yorodumi
- PDB-4rdi: Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rdi
TitleCrystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA
ComponentstRNA threonylcarbamoyladenosine dehydratase
KeywordsLIGASE / Rossmann Fold / Dehydratase
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 / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / tRNA threonylcarbamoyladenosine dehydratase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPark, S.Y. / Kim, S. / Lee, H.
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.
History
DepositionSep 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references

-
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)127,34212
Polymers124,9454
Non-polymers2,3978
Water10,989610
1
A: tRNA threonylcarbamoyladenosine dehydratase
B: tRNA threonylcarbamoyladenosine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6716
Polymers62,4732
Non-polymers1,1994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-26 kcal/mol
Surface area18550 Å2
MethodPISA
2
C: tRNA threonylcarbamoyladenosine dehydratase
D: tRNA threonylcarbamoyladenosine dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6716
Polymers62,4732
Non-polymers1,1994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-23 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.710, 97.036, 84.215
Angle α, β, γ (deg.)90.00, 111.83, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 31236.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tcdA, ygdL, csdL / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q46927, Ligases; Forming carbon-oxygen bonds
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 610 / 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: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% (w/v) PEG 3350, 0.1 M Tris, pH 8.5 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 70428 / % possible obs: 98.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 4.81 / Rsym value: 0.362 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.442 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20916 3545 5 %RANDOM
Rwork0.15631 ---
obs0.15897 66826 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0 Å2-0.55 Å2
2--0.08 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7286 0 148 610 8044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197575
X-RAY DIFFRACTIONr_bond_other_d0.0010.027418
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.98610281
X-RAY DIFFRACTIONr_angle_other_deg0.895316961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61723.401297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.201151186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2011560
X-RAY DIFFRACTIONr_chiral_restr0.1160.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021695
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_it2.4052.3313890
X-RAY DIFFRACTIONr_mcbond_other2.4052.333889
X-RAY DIFFRACTIONr_mcangle_it3.4093.4734850
X-RAY DIFFRACTIONr_mcangle_other3.4093.4754851
X-RAY DIFFRACTIONr_scbond_it3.3932.7583685
X-RAY DIFFRACTIONr_scbond_other3.3922.7583685
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0173.9565429
X-RAY DIFFRACTIONr_long_range_B_refined7.44620.1379118
X-RAY DIFFRACTIONr_long_range_B_other7.06519.6598800
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 271 -
Rwork0.195 4811 -
obs--96.98 %

+
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