[English] 日本語
Yorodumi
- PDB-2pqy: E. coli RNase 1 (in vitro refolded with DsbA only) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pqy
TitleE. coli RNase 1 (in vitro refolded with DsbA only)
ComponentsRibonuclease I
KeywordsHYDROLASE / ribonuclease
Function / homology
Function and homology information


Enterobacter ribonuclease / Enterobacter ribonuclease activity / ribonuclease T2 activity / RNA catabolic process / outer membrane-bounded periplasmic space / RNA binding / extracellular region / cytoplasm
Similarity search - Function
Ribonuclease T2, prokaryotic / Ribonuclease T2, His active site 1 / Ribonuclease T2 family histidine active site 1. / Ribonuclease T2-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily ...Ribonuclease T2, prokaryotic / Ribonuclease T2, His active site 1 / Ribonuclease T2 family histidine active site 1. / Ribonuclease T2-like / Ribonuclease T2 family / Ribonuclease Rh; Chain A / Ribonuclease T2-like / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Model detailsE. coli RNase 1 refolded in vitro by the aid of the disulfide oxidoreductase DsbA and shows that ...E. coli RNase 1 refolded in vitro by the aid of the disulfide oxidoreductase DsbA and shows that experimental condition involving tDsbA but not DsbC leads to its native structure
AuthorsMessens, J. / Loris, R.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The oxidase DsbA folds a protein with a nonconsecutive disulfide.
Authors: Messens, J. / Collet, J.F. / Van Belle, K. / Brosens, E. / Loris, R. / Wyns, L.
History
DepositionMay 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: Ribonuclease I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4283
Polymers27,1931
Non-polymers2352
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.571, 49.548, 53.328
Angle α, β, γ (deg.)90.000, 97.682, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ribonuclease I / Enterobacter ribonuclease / RNase I


Mass: 27192.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rna, rnsA / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl 21(DE3) PlysS / References: UniProt: P21338, EC: 3.1.27.6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.1 M MES pH 6.1, 0.1 M NH4AC, 10 % glycerol, 1 mM MgCl2, 25 % polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. all: 9192 / Num. obs: 9192 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rsym value: 0.073 / Net I/σ(I): 11.86
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.65 / Num. unique all: 979 / Rsym value: 0.281 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345data collection
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PQX

2pqx


Resolution: 2.3→15 Å / Cross valid method: THROUGHOUT / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 756 -random
Rwork0.196 ---
all-9192 --
obs-9192 100 %-
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 13 82 1916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.512

+
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://pdbjlvh1.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