+Open data
-Basic information
Entry | Database: PDB / ID: 3umt | ||||||
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Title | scFv12, Anti-BclA antibody single chain variable fragment | ||||||
Components | scFv heavy chain and light chain | ||||||
Keywords | IMMUNE SYSTEM / scFv / stability engineering / Anthrax / Anti-BclA antibody / Immunoglobulin fold (VH and VL domains) / Antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å | ||||||
Authors | Pokkuluri, P.R. | ||||||
Citation | Journal: To be Published Title: Systematic stability engineering of single-chain antibodies Authors: Wilton, R. / Londer, Y.Y. / Hanson, D.K. / Zerbs, S. / Dirks, A. / Warner, C. / Carney, J.P. / Pokkuluri, P.R. / Stevens, F.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3umt.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3umt.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 3umt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/3umt ftp://data.pdbj.org/pub/pdb/validation_reports/um/3umt | HTTPS FTP |
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-Related 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: 27448.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) | ||
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#2: Chemical | ChemComp-NHE / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | THE PROTEIN CRYSTALLIZSequence details | RESIDUES 3-121 CORRESPONDS TO VH DOMAIN AND RESIDUES 138-248 CORRESPOND TO THE VL DOMAIN. THE ...RESIDUES 3-121 CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 1M Sodium citrate, 0.1 M CHES pH9.5 diluted by water 4:1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97931 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.798→100 Å / Num. all: 22646 / Num. obs: 22608 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 60 |
Reflection shell | Resolution: 1.798→1.83 Å / Redundancy: 12 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 6.4 / Num. unique all: 1095 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: VH domain from structure 1KTR, VL domain from structure 1FGV Resolution: 1.798→30.914 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.358 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.798→30.914 Å
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Refine LS restraints |
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LS refinement shell |
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