[English] 日本語
Yorodumi
- PDB-5j5v: CdiA-CT from uropathogenic Escherichia coli in complex with cogna... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j5v
TitleCdiA-CT from uropathogenic Escherichia coli in complex with cognate immunity protein and CysK
Components
  • Cysteine synthase A
  • Immunity protein CdiI
  • tRNA nuclease CdiA
KeywordsTOXIN / complex / endonuclease / immunity protein
Function / homology
Function and homology information


S-carboxymethylcysteine synthase / S-carboxymethylcysteine synthase activity / cysteine synthase complex / tRNA-specific ribonuclease activity / L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / other organism cell membrane / cysteine biosynthetic process from serine / amino acid biosynthetic process ...S-carboxymethylcysteine synthase / S-carboxymethylcysteine synthase activity / cysteine synthase complex / tRNA-specific ribonuclease activity / L-cysteine desulfhydrase activity / cysteine synthase / cysteine synthase activity / other organism cell membrane / cysteine biosynthetic process from serine / amino acid biosynthetic process / RNA endonuclease activity / pyridoxal phosphate binding / transferase activity / toxin activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / tRNA binding / lyase activity / protein homodimerization activity / extracellular region / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Immunity protein CdiI / CDI immunity proteins / Bacterial toxin 28 / Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain ...Immunity protein CdiI / CDI immunity proteins / Bacterial toxin 28 / Toxin CdiA-like, Filamentous hemagglutinin motif repeats / VENN motif-containing domain / Pre-toxin domain with VENN motif / Hemagglutinin repeat / Hemagglutinin repeat / Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain / TPS secretion domain / haemagglutination activity domain / Cysteine synthase CysK / Cysteine synthase / Parallel beta-helix repeat / Parallel beta-helix repeats / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pectin lyase fold / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pectin lyase fold/virulence factor / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cysteine synthase A / Cysteine synthase A / tRNA nuclease CdiA / Immunity protein CdiI
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Escherichia coli O6:K15:H31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsGoulding, C.W. / Johnson, P.M. / Morse, R.P.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Unraveling the essential role of CysK in CDI toxin activation.
Authors: Johnson, P.M. / Beck, C.M. / Morse, R.P. / Garza-Sanchez, F. / Low, D.A. / Hayes, C.S. / Goulding, C.W.
History
DepositionApr 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2May 3, 2017Group: Non-polymer description
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine synthase A
B: tRNA nuclease CdiA
C: Immunity protein CdiI
D: Cysteine synthase A
E: tRNA nuclease CdiA
F: Immunity protein CdiI


Theoretical massNumber of molelcules
Total (without water)151,6036
Polymers151,6036
Non-polymers00
Water1,820101
1
A: Cysteine synthase A
B: tRNA nuclease CdiA
C: Immunity protein CdiI


Theoretical massNumber of molelcules
Total (without water)75,8013
Polymers75,8013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-23 kcal/mol
Surface area22880 Å2
MethodPISA
2
D: Cysteine synthase A
E: tRNA nuclease CdiA
F: Immunity protein CdiI


Theoretical massNumber of molelcules
Total (without water)75,8013
Polymers75,8013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-23 kcal/mol
Surface area23000 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-60 kcal/mol
Surface area41340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.251, 195.539, 175.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Cysteine synthase A / CSase A / O-acetylserine (thiol)-lyase A / OAS-TL A / O-acetylserine sulfhydrylase A / Sulfate ...CSase A / O-acetylserine (thiol)-lyase A / OAS-TL A / O-acetylserine sulfhydrylase A / Sulfate starvation-induced protein 5 / SSI5


Mass: 34726.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: cysK, Z3680, ECs3286 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0ABK6, UniProt: P0ABK5*PLUS, cysteine synthase
#2: Protein tRNA nuclease CdiA / tRNase CdiA / Toxin CdiA


Mass: 24841.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:K15:H31 (strain 536 / UPEC) (bacteria)
Strain: 536 / UPEC / Gene: cdiA, ECP_4580 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0T963, Hydrolases; Acting on ester bonds
#3: Protein Immunity protein CdiI


Mass: 16233.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O6:K15:H31 (strain 536 / UPEC) (bacteria)
Strain: 536 / UPEC / Gene: cdiI, ECP_4579 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0T964
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.1 M sodium cacodylate (pH 7.1), 0.2 M ammonium sulfate, 17% (w/v) PEG-8000

-
Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.75→48.825 Å / Num. obs: 36681 / % possible obs: 99.97 % / Redundancy: 14.5 % / Net I/σ(I): 10.41

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
PHENIX(Phaser-MR: 1.10.1_2155)phasing
PHENIX(AutoBuild: 1.10.1_2155)model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J43

5j43


Resolution: 2.75→48.825 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.54
RfactorNum. reflection% reflection
Rfree0.2481 914 2.49 %
Rwork0.1964 --
obs0.1976 36673 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→48.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8197 0 0 101 8298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118311
X-RAY DIFFRACTIONf_angle_d1.07211238
X-RAY DIFFRACTIONf_dihedral_angle_d14.4195130
X-RAY DIFFRACTIONf_chiral_restr0.0621309
X-RAY DIFFRACTIONf_plane_restr0.0071460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.8950.34971290.27335044X-RAY DIFFRACTION100
2.895-3.07630.29011280.24765029X-RAY DIFFRACTION100
3.0763-3.31380.3021300.23525074X-RAY DIFFRACTION100
3.3138-3.64720.24691300.20715081X-RAY DIFFRACTION100
3.6472-4.17470.25091300.17775086X-RAY DIFFRACTION100
4.1747-5.25870.20481310.16325142X-RAY DIFFRACTION100
5.2587-48.83240.22061360.18015303X-RAY DIFFRACTION100

+
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