[English] 日本語
Yorodumi
- PDB-6jgu: Crystal structure at atomic resolution reveals the catalytic mech... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jgu
TitleCrystal structure at atomic resolution reveals the catalytic mechanism in peptidyl-tRNA hydrolase from Acinetobacter baumannii.
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / protein quality control for misfolded or incompletely synthesized proteins / rescue of stalled ribosome / tRNA binding / 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
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsViswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure at atomic resolution reveals the catalytic mechanism in peptidyl-tRNA hydrolase from Acinetobacter baumannii.
Authors: Viswanathan, V. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-tRNA hydrolase


Theoretical massNumber of molelcules
Total (without water)21,2501
Polymers21,2501
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.964, 66.194, 75.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Peptidyl-tRNA hydrolase / PTH


Mass: 21250.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria)
Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81
Gene: pth, HMPREF0010_01329 / Production host: Escherichia coli (E. coli) / References: UniProt: D0C9L6, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.01 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 1500, 0.1M HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid), pH 7.5, 20% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97199 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97199 Å / Relative weight: 1
ReflectionResolution: 1.02→49.92 Å / Num. obs: 73420 / % possible obs: 88.37 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.039 / Net I/σ(I): 8.45
Reflection shellResolution: 1.022→1.049 Å / Rmerge(I) obs: 2.236 / Mean I/σ(I) obs: 0.756 / Num. unique obs: 6369 / CC1/2: 0.243 / Rpim(I) all: 0.983

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y9A

5y9a


Resolution: 1.02→49.91 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.953 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.026 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.15726 3778 4.9 %RANDOM
Rwork0.13671 ---
obs0.13772 73420 88.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.758 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0 Å20 Å2
2--0.58 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.02→49.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 0 233 1729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0121563
X-RAY DIFFRACTIONr_bond_other_d0.0070.0171538
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.6262120
X-RAY DIFFRACTIONr_angle_other_deg0.7451.5753511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0995205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.55722.59381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79115263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.316159
X-RAY DIFFRACTIONr_chiral_restr0.1150.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021842
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02385
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_it1.8660.958793
X-RAY DIFFRACTIONr_mcbond_other1.868792
X-RAY DIFFRACTIONr_mcangle_it2.1581.446992
X-RAY DIFFRACTIONr_mcangle_other2.15916.955993
X-RAY DIFFRACTIONr_scbond_it8.1991.357770
X-RAY DIFFRACTIONr_scbond_other8.2770
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4751.8581123
X-RAY DIFFRACTIONr_long_range_B_refined6.30814.2151792
X-RAY DIFFRACTIONr_long_range_B_other6.20713.3361735
X-RAY DIFFRACTIONr_rigid_bond_restr11.25831563
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.022→1.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 31 -
Rwork0.33 619 -
obs--10.21 %
Refinement TLS params.Method: refined / Origin x: 7.276 Å / Origin y: 8.874 Å / Origin z: 15.474 Å
111213212223313233
T0.0058 Å2-0.001 Å20.0001 Å2-0.0047 Å20.0001 Å2--0.004 Å2
L0.2967 °2-0.0827 °20.1184 °2-0.5146 °2-0.1039 °2--0.4509 °2
S0.006 Å °-0.0256 Å °-0.0038 Å °0.0127 Å °0.0226 Å °0.0364 Å °0.0003 Å °0.0147 Å °-0.0287 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 193
2X-RAY DIFFRACTION1A202 - 433

+
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