+Open data
-Basic information
Entry | Database: PDB / ID: 6be2 | ||||||
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Title | Crystal structure of a polysaccharide-binding human Fab (F598) | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin / human antibody / antigen binding fragment | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Soliman, C. / Ramsland, P.A. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structural basis for antibody targeting of the broadly expressed microbial polysaccharide poly-N-acetylglucosamine. Authors: Soliman, C. / Walduck, A.K. / Yuriev, E. / Richards, J.S. / Cywes-Bentley, C. / Pier, G.B. / Ramsland, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6be2.cif.gz | 190.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6be2.ent.gz | 149.1 KB | Display | PDB format |
PDBx/mmJSON format | 6be2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/6be2 ftp://data.pdbj.org/pub/pdb/validation_reports/be/6be2 | HTTPS FTP |
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-Related structure data
Related structure data | 6be3C 6be4C 3mlxS 4lldS 5eorS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 24176.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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#2: Antibody | Mass: 23120.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
#3: 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: 2.55 Å3/Da / Density % sol: 51.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 20% PEG 4000, 20% iso-propanol, 0.1 M sodium citrate pH5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→30.914 Å / Num. obs: 54253 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.055 / Net I/σ(I): 25.19 |
Reflection shell | Resolution: 1.69→1.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 3.08 / Num. unique obs: 8588 / CC1/2: 0.877 / Rrim(I) all: 0.877 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LLD, 5EOR, 3MLX Resolution: 1.7→30.914 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→30.914 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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