+Open data
-Basic information
Entry | Database: PDB / ID: 1ad9 | ||||||
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Title | IGG-FAB FRAGMENT OF ENGINEERED HUMAN MONOCLONAL ANTIBODY CTM01 | ||||||
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: 2.8 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 | 1ad9.cif.gz | 172.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ad9.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ad9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/1ad9 ftp://data.pdbj.org/pub/pdb/validation_reports/ad/1ad9 | HTTPS FTP |
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-Related structure data
Related structure data | 1ad0SC 1ae6C 1cloC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24161.998 Da / Num. of mol.: 2 / Fragment: CTM01 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: 468243 #2: Antibody | Mass: 23809.568 Da / Num. of mol.: 2 / Fragment: CTM01 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: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Sequence details | AMINO ACIDS ARE NUMBERED ACCORDING TO THE KABAT NUMBERING SYSTEM FOR ANTIBODIES (KABAT, E.A., WU, T. ...AMINO ACIDS ARE NUMBERED ACCORDING TO THE KABAT NUMBERING SYSTEM FOR ANTIBODIES | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 45.6 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.6 Details: 13-18% PEG4000/200-250MM LISO4, BUFFERED AT PH7.6 WITH 100MM TRIS | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996 / 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: 2.8→20 Å / Num. obs: 25776 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 34.5 Å2 / Rsym value: 0.105 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.8→3.02 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.377 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 143861 / Rmerge(I) obs: 0.105 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.377 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AD0 Resolution: 2.8→15 Å / Rfactor Rfree error: 0.008 / 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: 36.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→15 Å /
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.93 Å / Rfactor Rfree error: 0.033 / 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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