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Yorodumi- PDB-1ivl: THE DE NOVO DESIGN OF AN ANTIBODY COMBINING SITE: CRYSTALLOGRAPHI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ivl | ||||||
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Title | THE DE NOVO DESIGN OF AN ANTIBODY COMBINING SITE: CRYSTALLOGRAPHIC ANALYSIS OF THE VL DOMAIN CONFIRMS THE STRUCTURAL MODEL | ||||||
Components | IGG-KAPPA M29B FV (LIGHT CHAIN) | ||||||
Keywords | IMMUNOGLOBULIN | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ISOPROPYL ALCOHOL / : Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.17 Å | ||||||
Authors | Essen, L.-O. / Skerra, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: The de novo design of an antibody combining site. Crystallographic analysis of the VL domain confirms the structural model. Authors: Essen, L.O. / Skerra, A. #1: Journal: J.Chromatogr.,A / Year: 1993 Title: Single-Step Purification of a Bacterially Expressed Antibody FV Fragment by Immobilized Metal Affinity Chromatography in the Presence of Betaine Authors: Essen, L.-O. / Skerra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ivl.cif.gz | 49.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ivl.ent.gz | 39.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ivl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/1ivl ftp://data.pdbj.org/pub/pdb/validation_reports/iv/1ivl | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 8 / 2: CIS PROLINE - PRO A 95 / 3: CIS PROLINE - PRO B 8 / 4: CIS PROLINE - PRO B 95 / 5: RESIDUES ARG A 24 AND B 24 ARE PARTIALLY DISORDERED. |
-Components
#1: Antibody | Mass: 11664.921 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 196585 #2: Chemical | ChemComp-IPA / | #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE PRESENTED IN THIS ENTRY IS DESCRIBED IN THE JRNL ARTICLE LISTED ABOVE. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.31 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 16-22 ℃ / pH: 5.75 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.17 Å / Lowest resolution: 20 Å / Num. obs: 12009 / % possible obs: 91 % / Observed criterion σ(I): 2 / Num. measured all: 69140 / Rmerge(I) obs: 0.06 |
-Processing
Software |
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Refinement | Resolution: 2.17→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.17→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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