[English] 日本語
Yorodumi
- PDB-1xty: Crystal structure of Sulfolobus solfataricus peptidyl-tRNA hydrolase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xty
TitleCrystal structure of Sulfolobus solfataricus peptidyl-tRNA hydrolase
ComponentsPeptidyl-tRNA hydrolase
KeywordsHYDROLASE / mixed beta sheet
Function / homology
Function and homology information


peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / translation / cytosol
Similarity search - Function
Peptidyl-tRNA hydrolase, archaea / Peptidyl-tRNA hydrolase, PTH2 / Peptidyl-tRNA hydrolase PTH2 / Bit1 / Bit1 / Peptidyl-tRNA hydrolase II domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsFromant, M. / Schmitt, E. / Mechulam, Y. / Lazennec, C. / Plateau, P. / Blanquet, S.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal structure at 1.8 A resolution and identification of active site residues of Sulfolobus solfataricus peptidyl-tRNA hydrolase.
Authors: Fromant, M. / Schmitt, E. / Mechulam, Y. / Lazennec, C. / Plateau, P. / Blanquet, S.
History
DepositionOct 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2013Group: Structure summary
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Peptidyl-tRNA hydrolase
B: Peptidyl-tRNA hydrolase
C: Peptidyl-tRNA hydrolase
D: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,39012
Polymers52,6224
Non-polymers7698
Water8,971498
1
A: Peptidyl-tRNA hydrolase
B: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6956
Polymers26,3112
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-73 kcal/mol
Surface area11360 Å2
MethodPISA
2
C: Peptidyl-tRNA hydrolase
D: Peptidyl-tRNA hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6956
Polymers26,3112
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-72 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.816, 67.232, 85.352
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number4
Space group name H-MP1211
Detailschain A and B form a dimer chain C and D form dimer

-
Components

#1: Protein
Peptidyl-tRNA hydrolase / PTH


Mass: 13155.490 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: DSM1617 / Gene: pth / Plasmid: pET-pthS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-rosetta / References: UniProt: Q980V1, peptidyl-tRNA hydrolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.5 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 2.8
Details: 0.8Ml SO4, 1.6% PEG 8000, pH 2.8, VAPOR DIFFUSION, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2003
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 48937 / Num. obs: 48937 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.065
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.8 % / Num. unique all: 3544 / Rsym value: 0.112 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→46.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.224 2925 RANDOM
Rwork0.205 --
obs0.205 48488 -
all-48488 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.589 Å20 Å2-1.351 Å2
2--1.582 Å20 Å2
3----4.171 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 40 498 4218
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004984
X-RAY DIFFRACTIONc_angle_deg1.12346
LS refinement shellResolution: 1.8→1.81 Å
RfactorNum. reflection
Rfree0.3009 60
Rwork0.2546 -
obs-876

+
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