[English] 日本語
Yorodumi
- PDB-4nbi: D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nbi
TitleD-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 1.86 Angstrom resolution
ComponentsD-tyrosyl-tRNA(Tyr) deacylase
KeywordsHYDROLASE / DTD / DEACYLASE / DTD-like
Function / homology
Function and homology information


Gly-tRNA(Ala) hydrolase activity / D-tyrosyl-tRNA(Tyr) deacylase activity / D-aminoacyl-tRNA deacylase / tRNA metabolic process / tRNA binding / nucleotide binding / cytoplasm
Similarity search - Function
D-aminoacyl-tRNA deacylase DTD / D-Tyr-tRNA(Tyr) deacylase / D-tyrosyl-tRNA(Tyr) deacylase / D-aminoacyl-tRNA deacylase-like superfamily / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3'-deoxy-3'-(D-tyrosylamino)adenosine / TRIETHYLENE GLYCOL / D-aminoacyl-tRNA deacylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsAhmad, S. / Routh, S.B. / Kamarthapu, V. / Sankaranarayanan, R.
CitationJournal: Elife / Year: 2013
Title: Mechanism of chiral proofreading during translation of the genetic code.
Authors: Ahmad, S. / Routh, S.B. / Kamarthapu, V. / Chalissery, J. / Muthukumar, S. / Hussain, T. / Kruparani, S.P. / Deshmukh, M.V. / Sankaranarayanan, R.
History
DepositionOct 23, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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: D-tyrosyl-tRNA(Tyr) deacylase
B: D-tyrosyl-tRNA(Tyr) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4755
Polymers38,4662
Non-polymers1,0093
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-10 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.134, 65.743, 56.917
Angle α, β, γ (deg.)90.000, 93.300, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein D-tyrosyl-tRNA(Tyr) deacylase


Mass: 19233.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: DTD, PF11_0095 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8IIS0, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-D3Y / 3'-deoxy-3'-(D-tyrosylamino)adenosine


Mass: 429.430 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O5
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 38.32 % / Mosaicity: 1.277 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 32% PEG 3350, 0.6M sodium chloride, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 21, 2011 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→25 Å / Num. obs: 25156 / % possible obs: 98.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.075 / Χ2: 1.343 / Net I/σ(I): 24.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.86-1.936.40.28322830.859189.3
1.93-27.10.23724800.975198.1
2-2.097.10.19125251.083198.4
2.09-2.217.10.15325231.068198.8
2.21-2.347.20.12425041.233199.1
2.34-2.527.20.10225321.294199.5
2.52-2.787.20.07825691.334199.7
2.78-3.187.30.05825521.4841100
3.18-47.20.05125741.9291100
4-257.20.07626142.003199.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KNF

3knf


Resolution: 1.86→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.651 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1925 1276 5.1 %RANDOM
Rwork0.1677 ---
obs0.169 25154 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.35 Å2 / Biso mean: 30.665 Å2 / Biso min: 12.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å2-0.58 Å2
2--0 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 1.86→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 72 250 2915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022693
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9823633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8915311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.21325.504129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88115501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.761510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021992
LS refinement shellResolution: 1.861→1.909 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 71 -
Rwork0.236 1619 -
all-1690 -
obs--91.55 %

+
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