+Open data
-Basic information
Entry | Database: PDB / ID: 1ad0 | ||||||
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Title | FAB FRAGMENT OF ENGINEERED HUMAN MONOCLONAL ANTIBODY A5B7 | ||||||
Components |
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Keywords | IMMUNOGLOBULIN / FAB 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: 2.5 Å | ||||||
Authors | Banfield, M.J. / Brady, R.L. | ||||||
Citation | Journal: Proteins / Year: 1997 Title: VL:VH domain rotations in engineered antibodies: crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs. Authors: Banfield, M.J. / King, D.J. / Mountain, A. / Brady, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ad0.cif.gz | 171.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ad0.ent.gz | 139 KB | Display | PDB format |
PDBx/mmJSON format | 1ad0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ad0_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 1ad0_full_validation.pdf.gz | 463.3 KB | Display | |
Data in XML | 1ad0_validation.xml.gz | 32 KB | Display | |
Data in CIF | 1ad0_validation.cif.gz | 44.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/1ad0 ftp://data.pdbj.org/pub/pdb/validation_reports/ad/1ad0 | HTTPS FTP |
-Related structure data
Related structure data | 1ad9C 1ae6C 1cloSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: Antibody | Mass: 23182.686 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): NSO CELLS / Production host: Mus musculus (house mouse) / References: GenBank: 243868 #2: Antibody | Mass: 23830.668 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): NSO CELLS / Production host: Mus musculus (house mouse) #3: 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: 2.4 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: PEG6000/400 CACL2, BUFFERED AT PH6 WITH 40MM BIS-TRIS, pH 6.0 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. obs: 29480 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 33.3 Å2 / Rsym value: 0.054 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.5→2.69 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.179 / % possible all: 94 |
Reflection | *PLUS Num. measured all: 49216 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 94 % / Rmerge(I) obs: 0.179 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CLO Resolution: 2.5→15 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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