[English] 日本語
Yorodumi
- PDB-1jch: Crystal Structure of Colicin E3 in Complex with its Immunity Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jch
TitleCrystal Structure of Colicin E3 in Complex with its Immunity Protein
Components
  • COLICIN E3
  • COLICIN E3 IMMUNITY PROTEIN
KeywordsRIBOSOME INHIBITOR / HYDROLASE / TRANSLOCATION DOMAIN IS A BETA-JELLYROLL / THE RECEPTOR-BINDING DOMAIN IS A COILED COIL / THE RNASE DOMAIN IS A SIX-STRANDED ANTIPARALLEL BETA-SHEET. THE IMMUNITY PROTEIN IS A FOUR-STRANDED ANTIPARALLEL BETA SHEET FLANKED BY 3 HELICES ON ONE SIDE OF THE SHEET
Function / homology
Function and homology information


negative regulation of ion transmembrane transporter activity / extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / ribosome binding / Lyases; Phosphorus-oxygen lyases / endonuclease activity / killing of cells of another organism / transmembrane transporter binding / defense response to bacterium / RNA binding
Similarity search - Function
Helix Hairpins / Colicin E3-like ribonuclease domain / Ribonuclease domain of colicin e3 (Residues 456-551) / Cloacin immunity protein / Cloacin immunity protein family / Cloacin immunity protein superfamily / Cloacin immunity protein / Colicin E3-like ribonuclease domain / Colicin E3-like ribonuclease domain superfamily / Cytotoxic ...Helix Hairpins / Colicin E3-like ribonuclease domain / Ribonuclease domain of colicin e3 (Residues 456-551) / Cloacin immunity protein / Cloacin immunity protein family / Cloacin immunity protein superfamily / Cloacin immunity protein / Colicin E3-like ribonuclease domain / Colicin E3-like ribonuclease domain superfamily / Cytotoxic / S-type Pyocin / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / Chitinase A; domain 3 / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Colicin E3 / Colicin-E3 immunity protein
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.02 Å
AuthorsSoelaiman, S. / Jakes, K. / Wu, N. / Li, C. / Shoham, M.
CitationJournal: Mol.Cell / Year: 2001
Title: Crystal structure of colicin E3: implications for cell entry and ribosome inactivation.
Authors: Soelaiman, S. / Jakes, K. / Wu, N. / Li, C. / Shoham, M.
History
DepositionJun 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 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_database_remark / 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 / _pdbx_database_remark.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 BIOLOGICAL UNITS. THE FIRST BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS A+B AND HETGROUPS CIT 601 AND 602, GOL 701 AND 702 AND HOH RESIDUES NOT STARTING WITH A PREFIX 5000. THE SECOND BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS C+D AND HETGROUPS CIT 5601 AND 5602, GOL 5701 AND 5702 AND HOH RESIDUES STARTING WITH A PREFIX 5000.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,78212
Polymers135,6454
Non-polymers1,1378
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: COLICIN E3
B: COLICIN E3 IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3916
Polymers67,8232
Non-polymers5684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-25 kcal/mol
Surface area29470 Å2
MethodPISA
3
C: COLICIN E3
D: COLICIN E3 IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3916
Polymers67,8232
Non-polymers5684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-25 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.986, 195.733, 85.124
Angle α, β, γ (deg.)90.00, 113.22, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.99997, 0.00024, 0.00756), (-0.00024, -1, -0.00042), (0.00756, -0.00042, 0.99997)33.34507, 148.82249, -0.00929
DetailsCOLICIN E3 FORMS A DIMER IN SOLUTION AS WELL AS IN THE CRYSTALLINE STATE. THE SECOND MOLECULE IN THE ASYMMETRIC UNIT CAN BE GENERATED BY THE FOLLOWING MATRIX: -0.99997 0.00024 0.00756, -0.00024 -1.00000 -0.00042, 0.00756 -0.00042 0.99997, AND TRANSLATION VECTOR IN ANGSTROMS: 33.345 148.822 -0.009

-
Components

#1: Protein COLICIN E3 / E.C.3.1.21.- / RIBONUCLEASE / COLICIN E3 A CHAIN


Mass: 58043.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110
References: UniProt: P00646, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Protein COLICIN E3 IMMUNITY PROTEIN / IMME3 / MICROCIN E3 IMMUNITY PROTEIN / COLICIN E3 CHAIN B / immunity protein 2


Mass: 9779.565 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P02984
#3: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3.62 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: SODIUM CITRATE, CADMIUM ACETATE, ph 5.6, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
Conc.: 1 M / Common name: sodium citrate / Details: pH5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.037 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 3.02→20 Å / Num. all: 37014 / Num. obs: 37014 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 70.8 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3509 / % possible all: 86.4

-
Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.02→20.17 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2270567.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1127 3 %RANDOM
Rwork0.237 ---
all0.237 37014 --
obs0.237 37014 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.5511 Å2 / ksol: 0.26419 e/Å3
Displacement parametersBiso mean: 74.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.48 Å20 Å28.68 Å2
2---8.29 Å20 Å2
3---1.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-10 Å
Luzzati sigma a0.56 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.02→20.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8526 0 76 396 8998
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.41
X-RAY DIFFRACTIONc_mcbond_it11.061.5
X-RAY DIFFRACTIONc_mcangle_it15.832
X-RAY DIFFRACTIONc_scbond_it16.322
X-RAY DIFFRACTIONc_scangle_it20.872.5
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.297 80 2.6 %
Rwork0.323 2973 -
obs-2973 60.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIT.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMCIT.TOP
X-RAY DIFFRACTION5GLYCEROL.PARAMGLYCEROL.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.233 / Rfactor Rfree: 0.282
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 74.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.41
X-RAY DIFFRACTIONc_mcbond_it11.061.5
X-RAY DIFFRACTIONc_scbond_it16.322
X-RAY DIFFRACTIONc_mcangle_it15.832
X-RAY DIFFRACTIONc_scangle_it20.872.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.297 / % reflection Rfree: 2.6 % / Rfactor Rwork: 0.323

+
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