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- PDB-8dez: Abp2D Receptor Binding Domain ACICU -

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Basic information

Entry
Database: PDB / ID: 8dez
TitleAbp2D Receptor Binding Domain ACICU
ComponentsAbp2D Receptor Binding Domain
KeywordsCELL ADHESION / Chaperone usher pathway adhesin receptor binding domain
Function / homologyFimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / CITRATE ANION / P pilus assembly protein, pilin FimA
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsTamadonfar, K.O. / Pinkner, J.P. / Dodson, K.W. / Kalas, V. / 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
DepositionJun 21, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abp2D Receptor Binding Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3564
Polymers18,8821
Non-polymers4743
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.176, 51.176, 128.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Abp2D Receptor Binding Domain


Mass: 18882.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: ACICU / Gene: ACICU_01810 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: A0A7U3Y091
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Li2SO4, 0.1 M Sodium Citrate and 15% Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9762 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.29→47.53 Å / Num. obs: 41674 / % possible obs: 94.96 % / Redundancy: 2 % / Biso Wilson estimate: 10.38 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03965 / Rrim(I) all: 0.05607 / Rsym value: 0.05607 / Net I/σ(I): 15.57
Reflection shellResolution: 1.29→1.336 Å / Rmerge(I) obs: 0.6855 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5543 / CC1/2: 0.52 / Rrim(I) all: 0.9695 / % possible all: 65.35

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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: 3u4k

3u4k


Resolution: 1.29→47.53 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2057 2041 4.9 %
Rwork0.202 39616 -
obs0.2022 41657 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.01 Å2 / Biso mean: 14.6877 Å2 / Biso min: 6.58 Å2
Refinement stepCycle: final / Resolution: 1.29→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 41 104 1476
Biso mean--23.28 19.03 -
Num. residues----173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.29-1.320.3772840.3148162560
1.32-1.3530.3269910.3088215178
1.353-1.38960.32321360.2877238788
1.3896-1.43050.24761440.2658267798
1.4305-1.47670.25471540.23842708100
1.4767-1.52950.22061410.21232731100
1.5295-1.59070.21661250.20322768100
1.5907-1.66310.21961600.19642735100
1.6631-1.75080.22351440.18952745100
1.7508-1.86050.19751460.18582763100
1.8605-2.00420.19941370.1852797100
2.0042-2.20590.191430.18432790100
2.2059-2.5250.20161450.1932822100
2.525-3.18120.19821300.1982889100
3.1812-47.530.1671610.18813028100
Refinement TLS params.Method: refined / Origin x: -21.6547 Å / Origin y: 5.208 Å / Origin z: 10.7153 Å
111213212223313233
T0.092 Å20.0177 Å2-0.0096 Å2-0.0783 Å2-0.0116 Å2--0.0474 Å2
L0.4907 °20.3262 °2-0.3721 °2-0.8466 °2-0.6586 °2--1.736 °2
S0.0016 Å °-0.0052 Å °-0.0057 Å °0.0712 Å °0.0104 Å °0.0117 Å °-0.0491 Å °-0.0241 Å °-0.0095 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 501
2X-RAY DIFFRACTION1allA601
3X-RAY DIFFRACTION1allS1 - 189

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