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Yorodumi- PDB-3eyv: Anti-Lewis Y Fab fragment with Lewis Y antigen in the presence of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eyv | |||||||||
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Title | Anti-Lewis Y Fab fragment with Lewis Y antigen in the presence of zinc ions | |||||||||
Components | (hu3S193 Fab, ...) x 2 | |||||||||
Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / BETA BARREL / HUMANIZED ANTIBODY / ANTIGEN BINDING FRAGMENT | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Lewis Y antigen, alpha anomer Function and homology information | |||||||||
Biological species | MUS MUSCULUS (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Farrugia, W. / Scott, A.M. / Ramsland, P.A. | |||||||||
Citation | Journal: Plos One / Year: 2009 Title: A possible role for metallic ions in the carbohydrate cluster recognition displayed by a lewis y specific antibody. Authors: Farrugia, W. / Scott, A.M. / 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 | 3eyv.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eyv.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 3eyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eyv_validation.pdf.gz | 878.2 KB | Display | wwPDB validaton report |
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Full document | 3eyv_full_validation.pdf.gz | 905.4 KB | Display | |
Data in XML | 3eyv_validation.xml.gz | 36 KB | Display | |
Data in CIF | 3eyv_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/3eyv ftp://data.pdbj.org/pub/pdb/validation_reports/ey/3eyv | HTTPS FTP |
-Related structure data
Related structure data | 1s3kS 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
-Antibody , 2 types, 4 molecules LAHB
#1: Antibody | Mass: 24066.689 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: MURINE COMPLEMENTARITY DETERMINING REGIONS GRAFTED ONTO HUMAN FRAMEWORK AND CONSTANT GENE SEQUENCES Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: humanized / Cell (production host): NS0 MURINE MYELOMA CELLS / Production host: MUS MUSCULUS (house mouse) #2: Antibody | Mass: 23796.654 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: MURINE COMPLEMENTARITY DETERMINING REGIONS GRAFTED ONTO HUMAN FRAMEWORK AND CONSTANT GENE SEQUENCES Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: humanized / Cell (production host): NS0 MURINE MYELOMA CELLS / Production host: MUS MUSCULUS (house mouse) |
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-Sugars , 1 types, 1 molecules
#3: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Lewis Y antigen / alpha anomer |
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-Non-polymers , 3 types, 148 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | MURINE COMPLEMENT |
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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: 2.4 Å3/Da / Density % sol: 48.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 25% (v/v) PEG MONOMETHYL ETHER 550, 0.1M MES, 0.01M ZINC SULFATE, pH 6.5, VAPOR DIFFUSION, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 15, 2004 / Details: MIRRORS |
Radiation | Monochromator: OSMIC BLUE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. all: 31623 / Num. obs: 31623 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.073 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 3074 / Rsym value: 0.38 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S3K Resolution: 2.5→42.65 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 28.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→42.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.021
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