[English] 日本語
Yorodumi
- PDB-1tfk: Ribonuclease from Escherichia coli complexed with its inhibtor protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tfk
TitleRibonuclease from Escherichia coli complexed with its inhibtor protein
Components
  • Colicin D
  • Colicin D immunity protein
KeywordsTOXIN/TOXIN INHIBITOR / PROTEIN-PROTEIN COMPLEX / TOXIN-TOXIN INHIBITOR COMPLEX
Function / homology
Function and homology information


extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / RNA nuclease activity / killing of cells of another organism / defense response to bacterium
Similarity search - Function
Colicin D / Nuclear Transport Factor 2; Chain: A, - #200 / Colicin D immunity protein domain / Colicin D superfamily / Bacterial self-protective colicin-like immunity / Colicin D, C-terminal / Colicin D, C-terminal domain superfamily / Colicin D / Colicin D/E5 nuclease domain superfamily / S-type Pyocin ...Colicin D / Nuclear Transport Factor 2; Chain: A, - #200 / Colicin D immunity protein domain / Colicin D superfamily / Bacterial self-protective colicin-like immunity / Colicin D, C-terminal / Colicin D, C-terminal domain superfamily / Colicin D / Colicin D/E5 nuclease domain superfamily / S-type Pyocin / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / Nuclear Transport Factor 2; Chain: A, / Four Helix Bundle (Hemerythrin (Met), subunit A) / Roll / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Colicin-D immunity protein / Colicin-D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsYajima, S. / Nakanishi, K. / Takahashi, K. / Ogawa, T. / Kezuka, Y. / Hidaka, M. / Nonaka, T. / Ohsawa, K. / Masaki, H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Relation between tRNase activity and the structure of colicin D according to X-ray crystallography
Authors: Yajima, S. / Nakanishi, K. / Takahashi, K. / Ogawa, T. / Hidaka, M. / Kezuka, Y. / Nonaka, T. / Ohsawa, K. / Masaki, H.
History
DepositionMay 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Colicin D
B: Colicin D immunity protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6583
Polymers21,4622
Non-polymers1951
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.503, 58.503, 149.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

-
Components

#1: Protein Colicin D


Mass: 10831.103 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CDA / Production host: Escherichia coli (E. coli) / References: UniProt: P17998
#2: Protein Colicin D immunity protein / ImmD / Microcin D immunity protein


Mass: 10631.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Inhibitor protein / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CDI / Production host: Escherichia coli (E. coli) / References: UniProt: P11899
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


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


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.67 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, DTT, magnesium acetate, MES, MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97919, 0.97937, 0.98200
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 27, 2003
RadiationMonochromator: the rotated-inclined double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979191
20.979371
30.9821
ReflectionResolution: 2.1→23.1 Å / Num. all: 15888 / Num. obs: 15793 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.2 Å / % possible all: 99.3

-
Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→23.1 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.251 790 RANDOM
Rwork0.225 --
all0.243 15888 -
obs0.228 15793 -
Refinement stepCycle: LAST / Resolution: 2.1→23.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 12 241 1713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1

+
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