[English] 日本語
Yorodumi
- PDB-1xk9: Pseudomanas exotoxin A in complex with the PJ34 inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xk9
TitlePseudomanas exotoxin A in complex with the PJ34 inhibitor
ComponentsExotoxin A
KeywordsTRANSFERASE / toxin / ADP-ribosylation / inhibitor
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity
Similarity search - Function
Exotoxin A catalytic domain / Exotoxin A, binding / Exotoxin A, middle domain / Exotoxin A, middle domain superfamily / Exotoxin A catalytic / Exotoxin A binding / Exotoxin A, targeting / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Concanavalin A-like lectin/glucanase domain superfamily ...Exotoxin A catalytic domain / Exotoxin A, binding / Exotoxin A, middle domain / Exotoxin A, middle domain superfamily / Exotoxin A catalytic / Exotoxin A binding / Exotoxin A, targeting / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-P34 / Exotoxin A
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYates, S.P. / Taylor, P.J. / Joergensen, R. / Ferrraris, D. / Zhang, J. / Andersen, G.R. / Merrill, A.R.
CitationJournal: BIOCHEM.J. / Year: 2005
Title: Structure-function analysis of water-soluble inhibitors of the catalytic domain of exotoxin A from Pseudomonas aeruginosa
Authors: Yates, S.P. / Taylor, P.J. / Joergensen, R. / Ferrraris, D. / Zhang, J. / Andersen, G.R. / Merrill, A.R.
History
DepositionSep 28, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exotoxin A
B: Exotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5174
Polymers46,9262
Non-polymers5912
Water7,224401
1
A: Exotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7582
Polymers23,4631
Non-polymers2951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7582
Polymers23,4631
Non-polymers2951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.040, 78.680, 91.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Exotoxin A / NAD-dependent ADP-ribosyltransferase


Mass: 23463.156 Da / Num. of mol.: 2 / Fragment: catalytic fragment, PE24H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PE(delta)5-399 / Production host: Escherichia coli (E. coli) / Strain (production host): BB101
References: UniProt: P11439, NAD+-diphthamide ADP-ribosyltransferase
#2: Chemical ChemComp-P34 / N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE


Mass: 295.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.5 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: sodium citrate, DTT, NaAzid, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.046 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 2003
RadiationMonochromator: Bent germanium crystal, horizontally focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.046 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. all: 24276 / Num. obs: 24276 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 13.35
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 7.7 / Num. unique all: 5718 / % possible all: 100

-
Processing

Software
NameClassification
XDSdata scaling
XSCALEdata scaling
CNSrefinement
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AER

1aer


Resolution: 2.1→35 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.235 1236 random
Rwork0.213 --
all0.214 24316 -
obs0.213 24275 -
Refinement stepCycle: LAST / Resolution: 2.1→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3090 0 44 401 3535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5

+
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