[English] 日本語
Yorodumi
- PDB-7wt6: Crystal structure of full-length peptidyl-tRNA hydrolase from Myc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wt6
TitleCrystal structure of full-length peptidyl-tRNA hydrolase from Mycobacterium tuberculosis
ComponentsPeptidyl-tRNA hydrolaseAlternative ribosome-rescue factor B
KeywordsHYDROLASE / Enzyme classification / Peptidyl-tRNA
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / aminoacyl-tRNA hydrolase activity / translation / plasma membrane / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesMycobacteriaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsKulandaisamy, R. / Das, U. / Inampudi, K.K.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)EEQ/2016/000507 India
Department of Biotechnology (DBT, India)BT/PR34319/Med/29/1488/2019 India
CitationJournal: To Be Published
Title: Crystal structure of full-length peptidyl-tRNA hydrolase from Mycobacterium tuberculosis
Authors: Kulandaisamy, R. / Das, U. / Inampudi, K.K.
History
DepositionFeb 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,8041
Polymers21,8041
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9050 Å2
Unit cell
Length a, b, c (Å)36.581, 39.003, 123.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

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


Mass: 21803.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacteriaceae bacterium (bacteria) / Strain: H37Rv / Gene: pth / Production host: Escherichia coli (E. coli) / References: UniProt: P9WHN7, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293.15 K / Method: microbatch
Details: 25% (W/V) PEG 8000, 0.1M HEPES pH 7.5 5% (V/V) 2-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2021 / Details: Vertical CRL/ Horizontal Eliptical mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.937→37.201 Å / Num. obs: 13646 / % possible obs: 98.61 % / Redundancy: 8 % / Biso Wilson estimate: 18.92 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.055 / Rrim(I) all: 0.159 / Net I/σ(I): 11.4
Reflection shellResolution: 1.937→1.97 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 587 / CC1/2: 0.887 / Rpim(I) all: 0.29 / Rrim(I) all: 0.78 / % possible all: 87.7

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z2I

2z2i


Resolution: 1.94→37.2 Å / SU ML: 0.2299 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7634 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2145 729 5.34 %
Rwork0.1687 12915 -
obs0.1712 13638 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.58 Å2
Refinement stepCycle: LAST / Resolution: 1.94→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 0 218 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581454
X-RAY DIFFRACTIONf_angle_d0.79311965
X-RAY DIFFRACTIONf_chiral_restr0.0506215
X-RAY DIFFRACTIONf_plane_restr0.0057264
X-RAY DIFFRACTIONf_dihedral_angle_d6.7057878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-2.090.25181360.19182396X-RAY DIFFRACTION94.41
2.09-2.30.23911560.17712570X-RAY DIFFRACTION99.49
2.3-2.630.24261310.17182586X-RAY DIFFRACTION99.67
2.63-3.310.22461540.17252625X-RAY DIFFRACTION99.89
3.31-37.20.18181520.15682738X-RAY DIFFRACTION99.48

+
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