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- PDB-1ikp: Pseudomonas Aeruginosa Exotoxin A, P201Q, W281A mutant -

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Basic information

Entry
Database: PDB / ID: 1ikp
TitlePseudomonas Aeruginosa Exotoxin A, P201Q, W281A mutant
ComponentsEXOTOXIN A
KeywordsTRANSFERASE / all 3 EXOTOXIN A domains
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: 1.45 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. / Falbel, T.G. / McKay, D.B.
#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 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXOTOXIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9055
Polymers66,7881
Non-polymers1174
Water9,728540
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.910, 99.070, 58.630
Angle α, β, γ (deg.)90.00, 97.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 66787.820 Da / Num. of mol.: 1 / Mutation: W281A, P201Q
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.: 540 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.37 %
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 281.0K
Crystal grow
*PLUS
Details: Collier, R.J., (1982) J. Mol. Biol., 157, 413.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2000 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→59.76 Å / Num. all: 293233 / Num. obs: 116635 / % possible obs: 88.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.52 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 23.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 5.8 / Num. unique all: 3860 / Rsym value: 0.117 / % possible all: 58
Reflection
*PLUS
Lowest resolution: 60 Å / Num. measured all: 293233
Reflection shell
*PLUS
% possible obs: 58 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wild Type EXOTOXIN A, 1.62A

Resolution: 1.45→21.82 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 12268844.2 / 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
Rfree0.228 10852 10 %RANDOM
Rwork0.205 ---
all0.205 116635 --
obs0.205 108126 90.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.2689 Å2 / ksol: 0.373386 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å20 Å2-0.85 Å2
2--0.63 Å20 Å2
3---1.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→21.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4582 0 4 540 5126
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it1.821.5
X-RAY DIFFRACTIONc_mcangle_it2.822
X-RAY DIFFRACTIONc_scbond_it3.012
X-RAY DIFFRACTIONc_scangle_it4.682.5
LS refinement shellResolution: 1.45→1.52 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.298 1105 9.8 %
Rwork0.27 10158 -
obs-108126 75.7 %
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.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 60 Å / Num. reflection obs: 97274 / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07
X-RAY DIFFRACTIONc_mcbond_it1.821.5
X-RAY DIFFRACTIONc_scbond_it3.012
X-RAY DIFFRACTIONc_mcangle_it2.822
X-RAY DIFFRACTIONc_scangle_it4.682.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.299 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.27 / Rfactor obs: 0.27

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