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- PDB-1ikq: Pseudomonas Aeruginosa Exotoxin A, wild type -

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Basic information

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


NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

#1: Protein EXOTOXIN A / Pseudomonas exotoxin / 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 / Chloride


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 / Water


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

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Experimental details

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Experiment

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

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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.

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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

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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

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