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- PDB-1aer: DOMAIN III OF PSEUDOMONAS AERUGINOSA EXOTOXIN COMPLEXED WITH BETA-TAD -

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Basic information

Entry
Database: PDB / ID: 1aer
TitleDOMAIN III OF PSEUDOMONAS AERUGINOSA EXOTOXIN COMPLEXED WITH BETA-TAD
ComponentsEXOTOXIN A
KeywordsADP-RIBOSYLATION / TOXIN / TRANSFERASE / GLYCOSYLTRANSFERASE / NAD
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 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
ADENOSINE MONOPHOSPHATE / Chem-TAD / 2-(1,5-DIDEOXYRIBOSE)-4-AMIDO-THIAZOLE / Exotoxin A
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsLi, M. / Dyda, F. / Benhar, I. / Pastan, I. / Davies, D.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Crystal structure of the catalytic domain of Pseudomonas exotoxin A complexed with a nicotinamide adenine dinucleotide analog: implications for the activation process and for ADP ribosylation
Authors: Li, M. / Dyda, F. / Benhar, I. / Pastan, I. / Davies, D.R.
#1: 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.
#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.
History
DepositionDec 11, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Derived calculations / Structure summary / Category: pdbx_entry_details / struct_conn / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXOTOXIN A
B: EXOTOXIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0965
Polymers45,8372
Non-polymers1,2593
Water1,946108
1
A: EXOTOXIN A
B: EXOTOXIN A
hetero molecules

A: EXOTOXIN A
B: EXOTOXIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,19210
Polymers91,6744
Non-polymers2,5186
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)87.640, 87.640, 133.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein EXOTOXIN A


Mass: 22918.580 Da / Num. of mol.: 2 / Fragment: DOMAIN III OF PSEUDOMONAS TOXIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: PPED5-399 / Production host: Escherichia coli (E. coli)
References: UniProt: P11439, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-TAD / BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE


Mass: 667.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N7O13P2S
#3: Chemical ChemComp-TIA / 2-(1,5-DIDEOXYRIBOSE)-4-AMIDO-THIAZOLE


Mass: 244.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H12N2O4S
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsTHE SEQUENCE IN THIS ENTRY IS FROM 400 TO 613 FROM THAT OF THE COMPLETE TOXIN IN GENE BANK. THERE ...THE SEQUENCE IN THIS ENTRY IS FROM 400 TO 613 FROM THAT OF THE COMPLETE TOXIN IN GENE BANK. THERE ARE TWO MONOMERS IN THE ASYMMETRIC UNIT: MONOMER 1 FROM A 400 TO A 609 WITH BETA-TAD NUMBERED 700. RESIDUES A 458 - A 463 AND A 610 - A 613 ARE NOT DEFINED. MONOMER 2 IS FROM B 400 TO B 600 WITH THIAZOLE RIBOSE NUMBERED B 700 AND AMP B 701. RESIDUE NAME "TIA" IS GIVEN TO THIAZOLE RIBOSE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 50.2 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlPEIII1drop
210 mMTris-HCl1drop
30.15-0.2 M1dropNaCl
51.5 Msodium citrate1reservoir
640 mMNAD1reservoir
4reservoir solution1drop0.002 ml

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 22417 / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
% possible obs: 93.4 % / Redundancy: 4.7 %
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / % possible obs: 78.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.285 -10 %
Rwork0.196 --
obs0.196 21956 94.3 %
Displacement parametersBiso mean: 28.17 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 83 108 3214
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.048
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.37
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.861
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.37
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.861

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