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- PDB-9f1i: Crystal structure of a first-in-class antibody for alpha-1,6-fuco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9f1i | ||||||
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Title | Crystal structure of a first-in-class antibody for alpha-1,6-fucosylated prostate-specific antigen, target bound | ||||||
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![]() | IMMUNE SYSTEM / antibody / fab / prostate-specific antigen / PSA / fucosylation / diagnostic assay | ||||||
Function / homology | ![]() regulation of systemic arterial blood pressure / zymogen activation / secretory granule / serine-type endopeptidase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Halldorsson, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Development of a first-in-class antibody and a specific assay for alpha-1,6-fucosylated prostate-specific antigen. Authors: Halldorsson, S. / Hillringhaus, L. / Hojer, C. / Muranyi, A. / Schraeml, M. / Lange, M.S. / Tabares, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 450.8 KB | Display | ![]() |
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PDB format | ![]() | 306.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 39.9 KB | Display | |
Data in CIF | ![]() | 59.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9f18C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 4 molecules HILM
#1: Antibody | Mass: 23734.545 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 22957.355 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein/peptide / Sugars , 2 types, 4 molecules PQ
#3: Protein/peptide | Mass: 1114.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #4: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 803 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/PFX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PFX.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-EDO / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.44 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Tris-HCl pH 8.5, 6.25% v/v PEG 3350, 6.25% v/v PEG 4000, 6.25% v/v PEG 2000 and 6.25% v/v PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→52.24 Å / Num. obs: 155757 / % possible obs: 95.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 27.86 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.054 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.38→1.49 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7791 / CC1/2: 0.633 / Rrim(I) all: 1.169 / % possible all: 65.4 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→41.2 Å
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Refine LS restraints |
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LS refinement shell |
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