[English] 日本語
Yorodumi
- PDB-3ph0: Crystal structure of the heteromolecular chaperone, AscE-AscG, fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ph0
TitleCrystal structure of the heteromolecular chaperone, AscE-AscG, from the type III secretion system in Aeromonas hydrophila
Components
  • AscE
  • AscG
KeywordsCHAPERONE / Type III secretion system / chaperones AscE and AscG
Function / homology
Function and homology information


Type III secretion system YscG / Bacterial type II secretion system chaperone protein (type_III_yscG) / Type III secretion system, secretion protein E / Type III secretion system, cytoplasmic E component of needle / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1040 / Immunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily ...Type III secretion system YscG / Bacterial type II secretion system chaperone protein (type_III_yscG) / Type III secretion system, secretion protein E / Type III secretion system, cytoplasmic E component of needle / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1040 / Immunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsChatterjee, C. / Kumar, S. / Chakraborty, S. / Tan, Y.W. / Leung, K.Y. / Sivaraman, J. / Mok, Y.K.
CitationJournal: Plos One / Year: 2011
Title: Crystal structure of the heteromolecular chaperone, AscE-AscG, from the type III secretion system in Aeromonas hydrophila
Authors: Chatterjee, C. / Kumar, S. / Chakraborty, S. / Tan, Y.W. / Leung, K.Y. / Sivaraman, J. / Mok, Y.K.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AscE
C: AscG
B: AscE
D: AscG


Theoretical massNumber of molelcules
Total (without water)28,6674
Polymers28,6674
Non-polymers00
Water4,197233
1
A: AscE
C: AscG


Theoretical massNumber of molelcules
Total (without water)14,3332
Polymers14,3332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-16 kcal/mol
Surface area6560 Å2
MethodPISA
2
B: AscE
D: AscG


Theoretical massNumber of molelcules
Total (without water)14,3332
Polymers14,3332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-15 kcal/mol
Surface area6690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.159, 71.937, 86.735
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein AscE


Mass: 7572.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1EHA4
#2: Protein AscG


Mass: 6760.776 Da / Num. of mol.: 2 / Fragment: residues 1-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q1EHA2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 47.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mM Tris(pH 7.4), 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9792, 0.9794, 0.9640, 1.542
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.9641
41.5421
ReflectionResolution: 2.4→50 Å / Num. obs: 16865 / % possible obs: 99.8 % / Rsym value: 0.089
Reflection shellHighest resolution: 2.4 Å / Rsym value: 0.089 / % possible all: 99.8

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 2.4→20 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflection
Rfree0.2923 1601 7.9 %
Rwork0.239 --
obs-11163 82.9 %
Solvent computationBsol: 51.8285 Å2
Displacement parametersBiso max: 105.82 Å2 / Biso mean: 44.3555 Å2 / Biso min: 20.74 Å2
Baniso -1Baniso -2Baniso -3
1--12.993 Å20 Å20 Å2
2--2.061 Å20 Å2
3---10.931 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 0 233 1978
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

+
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://pdbjlvh1.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