[English] 日本語
Yorodumi
- PDB-1ikq: Pseudomonas Aeruginosa Exotoxin A, wild type -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ikq
TitlePseudomonas Aeruginosa Exotoxin A, wild type
ComponentsEXOTOXIN A
KeywordsTRANSFERASE / DOMAIN I / II / III of EXOTOXIN A
Function / homology
Function and homology information


symbiont-mediated suppression of host translation elongation / NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / symbiont-mediated killing of host cell / nucleotidyltransferase activity / toxin activity
Similarity search - Function
Exotoxin A, middle domain / Exotoxin A, middle domain / 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 ...Exotoxin A, middle domain / Exotoxin A, middle domain / 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 / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Alpha-Beta Complex / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsMcKay, D.B. / Wedekind, J.E. / Trame, C.B.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Refined Crystallographic Structure of Pseudomonas aeruginosa Exotoxin A and its Implications for the Molecular Mechanism of Toxicity
Authors: Wedekind, J.E. / Trame, C.B. / Dorywalska, M. / Koehl, P. / Raschke, T.M. / McKee, M. / FitzGerald, D. / Collier, R.J. / McKay, D.B.
#1: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallization of Exotoxin A from Pseudomonas aeruginosa
Authors: Collier, R.J. / McKay, D.B.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1986
Title: Structure of Exotoxin A of Pseudomonas aeruginosa at 3.0-Angstrom Resolution
Authors: Allured, V.S. / Collier, R.J. / Carroll, S.F. / McKay, D.B.
#3: Journal: Proteins / Year: 1988
Title: Mapping the Enzymatic Active Site of Pseudomonas aeruginosa Exotoxin A
Authors: Brandhuber, B.J. / Allured, V.S. / G., Falbel T. / B., McKay D.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: The Crystal Structure of Pseudomonas aeruginosa Exotoxin Domain III with Nicotinamide and AMP: conformational differences with the intact exotoxin
Authors: Li, M. / Dyda, F. / Benhar, I. / Pastan, I. / Davies, D.R.
History
DepositionMay 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EXOTOXIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9895
Polymers66,8721
Non-polymers1174
Water9,836546
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.520, 98.120, 58.260
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein EXOTOXIN A / NAD-DEPENDENT ADP-RIBOSYLTRANSFERASE


Mass: 66871.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PE / Plasmid: pMOA1A2VK352 f+ T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P11439, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, sodium chloride, hepes, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Details: Collier, R.J., (1982) J. Mol. Biol., 157, 413.

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
SYNCHROTRONSSRL BL7-121
Detector
TypeIDDetectorDateDetails
RIGAKU1IMAGE PLATEMar 4, 1998mirrors
MARRESEARCH2IMAGE PLATEJun 15, 1998double crystal monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
ReflectionResolution: 1.62→50 Å / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 21.4 Å2
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 80328 / % possible obs: 93 % / Num. measured all: 224879 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Highest resolution: 1.62 Å / Lowest resolution: 1.71 Å / % possible obs: 91 % / Rmerge(I) obs: 0.185

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A EXOTOXIN A model (ref. 3)

Resolution: 1.62→49.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1832154.15 / 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
Rfree0.235 6477 8.1 %RANDOM
Rwork0.209 ---
all0.2095 80287 --
obs0.209 80287 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.8 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.49 Å20 Å2-1.57 Å2
2--2.82 Å20 Å2
3---2.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.62→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 4 546 5187
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it2.51.5
X-RAY DIFFRACTIONc_mcangle_it3.992
X-RAY DIFFRACTIONc_scbond_it4.582
X-RAY DIFFRACTIONc_scangle_it6.922.5
LS refinement shellResolution: 1.62→1.69 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.32 728 7.8 %
Rwork0.286 8665 -
obs--89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE-WT.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection obs: 73810 / σ(F): 0 / % reflection Rfree: 8.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94
X-RAY DIFFRACTIONc_mcbond_it2.51.5
X-RAY DIFFRACTIONc_scbond_it4.582
X-RAY DIFFRACTIONc_mcangle_it3.992
X-RAY DIFFRACTIONc_scangle_it6.922.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / % reflection Rfree: 7.8 % / Rfactor Rwork: 0.286 / Rfactor obs: 0.286

+
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