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- PDB-8dka: Abp2D receptor binding domain R86E -

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Basic information

Entry
Database: PDB / ID: 8dka
TitleAbp2D receptor binding domain R86E
ComponentsAbp2D Receptor Binding Domain R86E
KeywordsCELL ADHESION / Chaperone usher pathway adhesin receptor binding domain
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus
Similarity search - Function
: / MrkD-like receptor binding domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily
Similarity search - Domain/homology
P pilus assembly protein, pilin FimA
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTamadonfar, K.O. / Pinkner, J.S. / Dodson, K.W. / Hultgren, S.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R37 AI048689-22 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)T32 AI007172-40 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Structure-function correlates of fibrinogen binding by Acinetobacter adhesins critical in catheter-associated urinary tract infections.
Authors: Tamadonfar, K.O. / Di Venanzio, G. / Pinkner, J.S. / Dodson, K.W. / Kalas, V. / Zimmerman, M.I. / Bazan Villicana, J. / Bowman, G.R. / Feldman, M.F. / Hultgren, S.J.
History
DepositionJul 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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: Abp2D Receptor Binding Domain R86E


Theoretical massNumber of molelcules
Total (without water)18,8541
Polymers18,8541
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.438, 51.847, 81.828
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Abp2D Receptor Binding Domain R86E


Mass: 18854.033 Da / Num. of mol.: 1 / Mutation: R86E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ACICU_01810 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: A0A7U3Y091
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M (NH4)2SO4, 20% Isopropanol, 16% PEG 4000, and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.072 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.9→43.8 Å / Num. obs: 12772 / % possible obs: 99.95 % / Redundancy: 7 % / Biso Wilson estimate: 22.32 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1146 / Rpim(I) all: 0.04693 / Rrim(I) all: 0.124 / Net I/σ(I): 15.46
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.8869 / Mean I/σ(I) obs: 3.17 / Num. unique obs: 1230 / CC1/2: 0.804 / CC star: 0.944 / Rpim(I) all: 0.3571 / Rrim(I) all: 0.9574 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DEZ

8dez


Resolution: 1.9→43.796 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 581 4.55 %
Rwork0.2117 12187 -
obs0.213 12768 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.67 Å2 / Biso mean: 31.5527 Å2 / Biso min: 11.86 Å2
Refinement stepCycle: final / Resolution: 1.9→43.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1238 0 0 25 1263
Biso mean---23.62 -
Num. residues----165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9001-2.09130.27171460.22922976
2.0913-2.39390.28641370.21973003
2.3939-3.01590.26231520.23783030
3.0159-43.7960.20851460.19373178
Refinement TLS params.Method: refined / Origin x: -9.6382 Å / Origin y: 13.156 Å / Origin z: -16.317 Å
111213212223313233
T0.1655 Å20.0244 Å2-0.0204 Å2-0.1359 Å2-0.0054 Å2--0.1524 Å2
L2.5955 °20.6426 °2-2.0421 °2-1.3185 °2-0.1282 °2--3.1835 °2
S-0.0614 Å °0.2345 Å °-0.0342 Å °-0.1894 Å °-0.0317 Å °0.0481 Å °0.0346 Å °-0.384 Å °0.0838 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 166
2X-RAY DIFFRACTION1allS1 - 53

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