+Open data
-Basic information
Entry | Database: PDB / ID: 8dka | |||||||||
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Title | Abp2D receptor binding domain R86E | |||||||||
Components | Abp2D Receptor Binding Domain R86E | |||||||||
Keywords | CELL ADHESION / Chaperone usher pathway adhesin receptor binding domain | |||||||||
Function / homology | Fimbrial-type adhesion domain / Fimbrial protein / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / pilus / cell adhesion / P pilus assembly protein, pilin FimA Function and homology information | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Tamadonfar, K.O. / Pinkner, J.S. / Dodson, K.W. / Hultgren, S.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dka.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dka.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 8dka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/8dka ftp://data.pdbj.org/pub/pdb/validation_reports/dk/8dka | HTTPS FTP |
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-Related structure data
Related structure data | 8dezSC 8df0C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.13 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.072 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Nov 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.67 Å2 / Biso mean: 31.5527 Å2 / Biso min: 11.86 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→43.796 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -9.6382 Å / Origin y: 13.156 Å / Origin z: -16.317 Å
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Refinement TLS group |
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