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- PDB-4z9d: EcPltA -

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Basic information

Entry
Database: PDB / ID: 4z9d
TitleEcPltA
ComponentsPertussis toxin-like subunit ArtA
KeywordsTRANSFERASE / UTEC / Escherichia coli / pertussis like / Membrane glycoproteins / Toxin / AB5 / Pertussis toxin / Typhoid toxin / Plt / PltAB / PltA / ribosyltransferase
Function / homologyBordetella pertussis toxin A / Pertussis toxin, subunit 1 / NAD+ ADP-ribosyltransferase activity / nucleotide binding / extracellular region / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pertussis toxin subunit 1
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLittler, D.R. / Johnson, M.D. / Summers, R.J. / Schembri, M.A. / Rossjohn, J. / Beddoe, T.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure and function analyses of a pertussis-like toxin from pathogenic Escherichia coli reveal a distinct mechanism of inhibition of trimeric G proteins.
Authors: Littler, D.R. / Ang, S.Y. / Moriel, D.G. / Kocan, M. / Kleifeld, O. / Johnson, M.D. / Tran, M.T. / Paton, A.W. / Paton, J.C. / Summers, R. / Schrembri, M. / Rossjohn, J. / Beddoe, T.T.
History
DepositionApr 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pertussis toxin-like subunit ArtA
B: Pertussis toxin-like subunit ArtA
C: Pertussis toxin-like subunit ArtA
D: Pertussis toxin-like subunit ArtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,72710
Polymers79,0284
Non-polymers2,7006
Water10,773598
1
A: Pertussis toxin-like subunit ArtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4433
Polymers19,7571
Non-polymers6862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pertussis toxin-like subunit ArtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4433
Polymers19,7571
Non-polymers6862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pertussis toxin-like subunit ArtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4202
Polymers19,7571
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pertussis toxin-like subunit ArtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4202
Polymers19,7571
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Pertussis toxin-like subunit ArtA
D: Pertussis toxin-like subunit ArtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8645
Polymers39,5142
Non-polymers1,3503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-27 kcal/mol
Surface area16850 Å2
MethodPISA
6
B: Pertussis toxin-like subunit ArtA
C: Pertussis toxin-like subunit ArtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8645
Polymers39,5142
Non-polymers1,3503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-22 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.520, 55.660, 73.060
Angle α, β, γ (deg.)90.06, 104.07, 96.17
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Pertussis toxin-like subunit ArtA / / Pertussis toxin-like subunit PltA


Mass: 19756.875 Da / Num. of mol.: 4 / Fragment: UNP residues 19-190 / Mutation: Q116D, E118D
Source method: isolated from a genetically manipulated source
Details: UPEC strain PA26B was isolated from a patient presenting with a urinary tract infection at the Princess Alexandra Hospital.
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PA26B / Gene: PU15_14675, PU38_26245 / Plasmid: pET28-NKI / Details (production host): hexahistidine tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B1KWV6, EC: 2.2.2.30
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.3 %
Description: Clusters of plate-like crystals that grew within 2-3 days
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Treated with 20 mM NAD+ for thirty minutes prior to crystallization, 1:1 protein to 4-7% PEG, 0.1 M Tris, pH 8.5, 0.15 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→70.8 Å / Num. all: 91849 / Num. obs: 55479 / % possible obs: 88.5 % / Redundancy: 1.7 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.6 / % possible all: 87.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4Z9C

4z9c


Resolution: 1.8→35.894 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 2818 5.08 %Random selection
Rwork0.1809 ---
obs0.1832 55466 88.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→35.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 178 598 6345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075926
X-RAY DIFFRACTIONf_angle_d1.1798085
X-RAY DIFFRACTIONf_dihedral_angle_d16.3852368
X-RAY DIFFRACTIONf_chiral_restr0.052861
X-RAY DIFFRACTIONf_plane_restr0.0061067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8310.31551360.26112591X-RAY DIFFRACTION87
1.831-1.86430.32611350.24822614X-RAY DIFFRACTION88
1.8643-1.90020.28831460.22662609X-RAY DIFFRACTION89
1.9002-1.9390.27321580.21482659X-RAY DIFFRACTION89
1.939-1.98110.23011560.19982644X-RAY DIFFRACTION89
1.9811-2.02720.2231470.19182682X-RAY DIFFRACTION90
2.0272-2.07790.24541320.18082676X-RAY DIFFRACTION90
2.0779-2.13410.25051440.18582721X-RAY DIFFRACTION91
2.1341-2.19690.22311430.18012681X-RAY DIFFRACTION90
2.1969-2.26780.23551370.17672687X-RAY DIFFRACTION90
2.2678-2.34880.23941350.17592748X-RAY DIFFRACTION91
2.3488-2.44280.20981350.1732674X-RAY DIFFRACTION90
2.4428-2.5540.22491280.17692666X-RAY DIFFRACTION90
2.554-2.68860.25861390.19262671X-RAY DIFFRACTION89
2.6886-2.8570.25831370.19472628X-RAY DIFFRACTION89
2.857-3.07740.2361370.19192635X-RAY DIFFRACTION88
3.0774-3.38690.22091470.17622588X-RAY DIFFRACTION87
3.3869-3.87650.20431460.15422479X-RAY DIFFRACTION84
3.8765-4.88210.1721370.14562478X-RAY DIFFRACTION83
4.8821-35.90110.17681430.16232517X-RAY DIFFRACTION85

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