+Open data
-Basic information
Entry | Database: PDB / ID: 8df0 | |||||||||
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Title | Abp1D receptor binding domain | |||||||||
Components | Abp1D Receptor Binding Domain | |||||||||
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 / Fimbria adhesin protein Function and homology information | |||||||||
Biological species | Acinetobacter baumannii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 8df0.cif.gz | 192.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8df0.ent.gz | 156.7 KB | Display | PDB format |
PDBx/mmJSON format | 8df0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/8df0 ftp://data.pdbj.org/pub/pdb/validation_reports/df/8df0 | HTTPS FTP |
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-Related structure data
Related structure data | 8dezSC 8dkaC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18846.119 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: fimA, AYR68_10060, B7L45_11295, BAA1790NC_1605, BS065_10665, CBL15_10290, CTZ19_10795, D8O08_010130, DLI72_16175, E2532_11475, E2533_08890, E2534_05850, E2535_07595, E2536_00985, E2538_06840, ...Gene: fimA, AYR68_10060, B7L45_11295, BAA1790NC_1605, BS065_10665, CBL15_10290, CTZ19_10795, D8O08_010130, DLI72_16175, E2532_11475, E2533_08890, E2534_05850, E2535_07595, E2536_00985, E2538_06840, E2539_15695, E2540_01165, E2541_05705, EA720_002470, FE003_11010, H1058_10155, HIN86_11385, IAG11_17165, SAMEA104305340_00065 Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: A0A219C937 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.96 Å3/Da / Density % sol: 75.21 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, hanging drop / Details: 0.8 M (NH4)2SO4, 0.025 M Citric Acid pH 3.56 |
-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: 0.9762 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Oct 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→44.51 Å / Num. obs: 45137 / % possible obs: 99.76 % / Redundancy: 13.9 % / Biso Wilson estimate: 33.97 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.2715 / Rpim(I) all: 0.07507 / Rrim(I) all: 0.2818 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 14 % / Rmerge(I) obs: 2.938 / Num. unique obs: 4370 / CC1/2: 0.434 / CC star: 0.778 / Rpim(I) all: 0.8113 / Rrim(I) all: 3.049 / % possible all: 99.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8DEZ Resolution: 2.1→44.51 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.8 / 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: 93.76 Å2 / Biso mean: 42.8553 Å2 / Biso min: 23.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→44.51 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -5.6049 Å / Origin y: 21.9195 Å / Origin z: -22.4341 Å
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Refinement TLS group |
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