+Open data
-Basic information
Entry | Database: PDB / ID: 1a5f | ||||||
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Title | FAB FRAGMENT OF A MONOCLONAL ANTI-E-SELECTIN ANTIBODY | ||||||
Components |
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Keywords | IMMUNOGLOBULIN / FAB / ANTIBODY / ANTI-E-SELECTIN | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Rodriguez-Romero, A. / Almog, O. / Tordova, M. / Randhawa, Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Primary and tertiary structures of the Fab fragment of a monoclonal anti-E-selectin 7A9 antibody that inhibits neutrophil attachment to endothelial cells. Authors: Rodriguez-Romero, A. / Almog, O. / Tordova, M. / Randhawa, Z. / Gilliland, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a5f.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a5f.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a5/1a5f ftp://data.pdbj.org/pub/pdb/validation_reports/a5/1a5f | HTTPS FTP |
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-Related structure data
Related structure data | 1bbdS 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
#1: Antibody | Mass: 24286.814 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: SP-20 FUSION MOUSE-MOUSE HYBRIDOMA / References: GenBank: 208622 |
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#2: Antibody | Mass: 23080.766 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: SP-20 FUSION MOUSE-MOUSE HYBRIDOMA |
#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: 2.6 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.8 Å / Num. obs: 10993 / % possible obs: 86.5 % / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 4.6 |
Reflection | *PLUS Num. measured all: 42928 / Rmerge(I) obs: 0.069 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BBD Resolution: 2.8→7 Å / Isotropic thermal model: GROUP / σ(F): 2
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Displacement parameters | Biso mean: 14.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.96 Å / Total num. of bins used: 6 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 9420 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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