[English] 日本語
Yorodumi
- PDB-1e44: ribonuclease domain of colicin E3 in complex with its immunity protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1.0E+44
Titleribonuclease domain of colicin E3 in complex with its immunity protein
Components
  • COLICIN E3
  • IMMUNITY PROTEIN
KeywordsRIBONUCLEASE / INHIBITION / PROTEIN-PROTEIN INTERACTIONS / RIBOSOME INACTIVATION / TOXIN
Function / homology
Function and homology information


negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / ion channel binding / endonuclease activity / cytolysis / Hydrolases, Acting on ester bonds / pathogenesis ...negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / ion channel binding / endonuclease activity / cytolysis / Hydrolases, Acting on ester bonds / pathogenesis / defense response to bacterium / RNA binding
Colicin E3-like ribonuclease domain / Cloacin immunity protein / Cloacin immunity protein superfamily / Pyosin/cloacin translocation domain superfamily / Cloacin colicin family / Colicin, receptor domain / Pyosin/cloacin translocation domain / Colicin-like bacteriocin tRNase domain / Cloacin immunity protein family / Colicin E3-like ribonuclease domain superfamily ...Colicin E3-like ribonuclease domain / Cloacin immunity protein / Cloacin immunity protein superfamily / Pyosin/cloacin translocation domain superfamily / Cloacin colicin family / Colicin, receptor domain / Pyosin/cloacin translocation domain / Colicin-like bacteriocin tRNase domain / Cloacin immunity protein family / Colicin E3-like ribonuclease domain superfamily / Coiled-coil receptor-binding R-domain of colicin E2 / Cytotoxic
Colicin-E3 / Colicin-E3 immunity protein
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsCarr, S. / Walker, D. / James, R. / Kleanthous, C. / Hemmings, A.M.
CitationJournal: Structure / Year: 2000
Title: Inhibition of a Ribosome Inactivating Ribonuclease: The Crystal Structure of the Cytotoxic Domain of Colicin E3 in Complex with its Immunity Protein
Authors: Carr, S. / Walker, D. / James, R. / Kleanthous, C. / Hemmings, A.M.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IMMUNITY PROTEIN
B: COLICIN E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7853
Polymers20,7232
Non-polymers621
Water3,081171
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-13.6 kcal/mol
Surface area10960 Å2
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)93.700, 93.700, 76.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein/peptide IMMUNITY PROTEIN /


Mass: 9910.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02984
#2: Protein/peptide COLICIN E3


Mass: 10812.117 Da / Num. of mol.: 1 / Fragment: RIBONUCLEASE DOMAIN RESIDUES 456-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli)
Description: CO-EXPRESSED WITH A HIS-TAGGED IMMUNITY PROTEIN
Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00646
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Ethylene glycol
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.39 Å3/Da / Density % sol: 72 %
Crystal growpH: 5.6
Details: 0.1 M NA CITRATE PH 5.6, 20% ISOPROPANOL, 10% PEG 4000
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Carr, S., (1999) Acta Crystallogr., D56, 1630.
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-ID
145-50 mg/mlproteindrop
210 mMTris-HCldrop
30.1 Msodium citratereservoir
420 %(v/v)PEG4000reservoir
520 %(v/v)2-propanolreservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9, 0.97, 0.979
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.971
30.9791
ReflectionResolution: 2.4→20 Å / Num. obs: 14892 / % possible obs: 98.7 % / Redundancy: 3 % / Rsym value: 0.039 / Net I/σ(I): 37.8
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.237 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 97.5 % / Rmerge(I) obs: 0.237

-
Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→30 Å / Data cutoff high absF: 100000 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.228 726 5 %
Rwork0.192 --
Obs0.192 14892 97.5 %
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 4 171 1633
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.86
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 2
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.45 Å / Rfactor Rfree: 0.229 / Rfactor obs: 0.194

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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