[English] 日本語
Yorodumi
- PDB-3vjr: Crystal structure of Peptidyl-tRNA hydrolase from Escherichia col... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vjr
TitleCrystal structure of Peptidyl-tRNA hydrolase from Escherichia coli in complex with the CCA-acceptor-T[PSI]C domain of tRNA
Components
  • Peptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B
  • tRNA CCA-acceptor
Keywordshydrolase/RNA / Peptidyl-tRNA hydrolase / CCA-acceptor-T[PSI]C domain / seven beta-strands form / hydrolase-RNA complex
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / translation / cytoplasm
Similarity search - Function
Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase signature 2. / Peptidyl-tRNA hydrolase signature 1. / Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase, conserved site / Peptidyl-tRNA hydrolase superfamily / Peptidyl-tRNA hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsIto, K. / Murakami, R. / Mochizuki, M. / Qi, H. / Shimizu, Y. / Miura, K.I. / Ueda, T. / Uchiumi, T.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural basis for the substrate recognition and catalysis of peptidyl-tRNA hydrolase.
Authors: Ito, K. / Murakami, R. / Mochizuki, M. / Qi, H. / Shimizu, Y. / Miura, K. / Ueda, T. / Uchiumi, T.
History
DepositionOct 28, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase
B: tRNA CCA-acceptor
C: Peptidyl-tRNA hydrolase
D: tRNA CCA-acceptor


Theoretical massNumber of molelcules
Total (without water)65,8574
Polymers65,8574
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-40 kcal/mol
Surface area27680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.070, 55.070, 413.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Peptidyl-tRNA hydrolase / Alternative ribosome-rescue factor B / PTH


Mass: 21395.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pth, b1204, JW1195 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7D1, peptidyl-tRNA hydrolase
#2: RNA chain tRNA CCA-acceptor


Mass: 11532.882 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA WAS REPEATED BY IN VITRO TRANSCRIPTION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 100mM acetate buffer, 20% (w/v) 1,4-butanediol, 30mM glycyl-glycyl-glycine , pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 27129 / Num. obs: 27129 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.056 / Rsym value: 0.059 / Net I/σ(I): 24.94
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 8.2 / Num. unique all: 4136 / Rsym value: 0.2 / % possible all: 93.7

-
Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PTH

2pth


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 15.482 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23657 1390 5 %RANDOM
Rwork0.19251 ---
all0.19472 26216 --
obs0.19472 26216 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.222 Å2
Baniso -1Baniso -2Baniso -3
1-3.14 Å21.57 Å20 Å2
2--3.14 Å20 Å2
3----4.72 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 1532 0 139 4631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214734
X-RAY DIFFRACTIONr_angle_refined_deg1.3662.3716752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4035384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9423.333132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.815504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2571522
X-RAY DIFFRACTIONr_chiral_restr0.0770.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213046
X-RAY DIFFRACTIONr_mcbond_it0.4881.51908
X-RAY DIFFRACTIONr_mcangle_it0.93623042
X-RAY DIFFRACTIONr_scbond_it1.332826
X-RAY DIFFRACTIONr_scangle_it2.0254.53710
LS refinement shellResolution: 2.399→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 103 -
Rwork0.258 1865 -
obs-1968 99.14 %
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)
11.51360.0314-0.13762.1424-0.05232.337-0.1280.0327-0.0498-0.05-0.03280.10250.19580.06410.16080.1583-0.08430.03310.0651-0.02930.1091-22.07679.79091.8265
20.57980.06070.26170.49111.03662.77150.03020.03820.1209-0.0403-0.0637-0.0696-0.2018-0.21910.03350.1711-0.0706-0.03070.1066-0.00340.1483-18.224932.5519-3.273
32.0477-0.1790.2291.74530.09512.2009-0.0381-0.0871-0.0674-0.0041-0.12070.1046-0.1642-0.13660.15880.0214-0.0020.01810.2131-0.04420.1143-30.116423.6566-40.8329
40.560.1822-1.02960.2889-0.25842.4748-0.06760.00380.01790.05410.0151-0.14170.33930.04770.05250.1107-0.00430.01310.22620.01210.1663-8.346415.581-35.8746
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 197
2X-RAY DIFFRACTION2B1 - 36
3X-RAY DIFFRACTION3C5 - 197
4X-RAY DIFFRACTION4D1 - 36

+
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