[English] 日本語
Yorodumi
- PDB-5kh1: Shigella flexneri Effector IpaH1880 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kh1
TitleShigella flexneri Effector IpaH1880
ComponentsInvasion plasmid antigen
KeywordsLIGASE / Shigella / Effector / E3 Ligase / Ubiquitin
Function / homology
Function and homology information


: / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / host cell cytoplasm / extracellular region
Similarity search - Function
Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
RING-type E3 ubiquitin transferase
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsNishide, A. / Mizushima, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Grant-in-Aid for Scientific Research (B)15H04341 Japan
Grant-in-Aid for JSPS Fellows14J10879 Japan
CitationJournal: To Be Published
Title: Shigella flexneri Effector IpaH1880
Authors: Nishide, A. / Mizushima, T.
History
DepositionJun 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Invasion plasmid antigen


Theoretical massNumber of molelcules
Total (without water)66,8601
Polymers66,8601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area29520 Å2
Unit cell
Length a, b, c (Å)56.316, 80.058, 298.346
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Invasion plasmid antigen


Mass: 66859.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaH_4, SF1880 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q83R64

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.07 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.1%(w/v) Tacsimate pH6.0 100mM Bis-Tris/HCl pH6.5 16% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 9062 / % possible obs: 92.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 92.8779608153 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.3
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.533 / % possible all: 86.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
BUCCANEERmodel building
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CVR

3cvr


Resolution: 3.4→44.011 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3046 471 5.22 %RANDOM
Rwork0.2388 ---
obs0.2423 9019 92.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→44.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4421 0 0 0 4421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114514
X-RAY DIFFRACTIONf_angle_d1.7116147
X-RAY DIFFRACTIONf_dihedral_angle_d19.7132750
X-RAY DIFFRACTIONf_chiral_restr0.07697
X-RAY DIFFRACTIONf_plane_restr0.009809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4003-3.89210.36321410.29872579X-RAY DIFFRACTION86
3.8921-4.90260.34881550.25342837X-RAY DIFFRACTION93
4.9026-44.01460.26251750.21163132X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.4278 Å / Origin y: -6.016 Å / Origin z: -38.3649 Å
111213212223313233
T0.7069 Å2-0.065 Å2-0.0321 Å2-0.7777 Å2-0.0258 Å2--0.5475 Å2
L0.1978 °2-0.0744 °2-0.0535 °2-1.1174 °2-1.6377 °2--2.0759 °2
S-0.0182 Å °0.4869 Å °-0.0352 Å °-0.3856 Å °-0.0041 Å °0.0103 Å °0.4116 Å °-0.0994 Å °-0.001 Å °
Refinement TLS groupSelection details: all

+
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