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Yorodumi- PDB-1b6d: BENCE JONES PROTEIN DEL: AN ENTIRE IMMUNOGLOBULIN KAPPA LIGHT-CHA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b6d | ||||||
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Title | BENCE JONES PROTEIN DEL: AN ENTIRE IMMUNOGLOBULIN KAPPA LIGHT-CHAIN DIMER | ||||||
Components | IMMUNOGLOBULINAntibody | ||||||
Keywords | IMMUNOGLOBULIN / KAPPA LIGHT-CHAIN DIMER | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | ||||||
Authors | Roussel, A. / Spinelli, S. / Deret, S. / Aucouturier, P. / Cambillau, C. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 1999 Title: The structure of an entire noncovalent immunoglobulin kappa light-chain dimer (Bence-Jones protein) reveals a weak and unusual constant domains association. Authors: Roussel, A. / Spinelli, S. / Deret, S. / Navaza, J. / Aucouturier, P. / Cambillau, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b6d.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b6d.ent.gz | 88 KB | Display | PDB format |
PDBx/mmJSON format | 1b6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/1b6d ftp://data.pdbj.org/pub/pdb/validation_reports/b6/1b6d | HTTPS FTP |
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-Related structure data
Related structure data | 1reiS 2bjl 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: 23011.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: IMMUNOGLOBULIN LIGHT-CHAIN DIMER / Source: (natural) Homo sapiens (human) / Organ: KIDNEY / Secretion: URINE / References: GenBank: 4768677 #2: 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: 2.77 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.74→10 Å / Num. obs: 12960 / % possible obs: 97.4 % / Redundancy: 4.5 % / Rsym value: 0.069 |
Reflection shell | Highest resolution: 2.74 Å / Rsym value: 0.285 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1REI, 2BJL Resolution: 2.74→6 Å / σ(F): 0
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Displacement parameters | Biso mean: 24.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.74→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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