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- PDB-2omn: Bence Jones KWR Protein- Immunoglobulin Light Chain Dimer, P4(3)2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2omn | |||||||||
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Title | Bence Jones KWR Protein- Immunoglobulin Light Chain Dimer, P4(3)2(1)2 Crystal Form | |||||||||
![]() | Bence Jones KWR Protein - Immunoglobulin Light Chain | |||||||||
![]() | IMMUNE SYSTEM / Immunoglobulin Light Chain | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHENOL![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Makino, D.L. / Larson, S.B. / McPherson, A. | |||||||||
![]() | ![]() Title: Bence Jones KWR protein structures determined by X-ray crystallography. Authors: Makino, D.L. / Henschen-Edman, A.H. / Larson, S.B. / McPherson, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.1 KB | Display | ![]() |
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PDB format | ![]() | 71.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.1 KB | Display | ![]() |
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Full document | ![]() | 467.5 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2oldC ![]() 2ombC ![]() 1dclS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 22698.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: urine / Source: (natural) ![]() #2: Chemical | #3: Chemical | ChemComp-IPH / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.5M Ammonium Sulfate, 0.1M Tris/HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 11, 2003 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→46.88 Å / Num. all: 20595 / Num. obs: 20595 / % possible obs: 76.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 35.1 Å2 / Limit h max: 32 / Limit h min: 0 / Limit k max: 18 / Limit k min: 0 / Limit l max: 73 / Limit l min: 0 / Observed criterion F max: 229355.06 / Observed criterion F min: 0.27 / Rsym value: 0.059 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 2.08→2.16 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 394 / Rsym value: 0.336 / % possible all: 15.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DCL Resolution: 2.2→45 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: PARAMETERS FOR PYROGLUTAMIC ACID AND PHENOL WERE OBTAINED FROM HETERO-COMPOUND INFORMATION CENTRE - UPPSALA.
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 37.1035 Å2 / ksol: 0.337824 e/Å3 | |||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.05 Å2 / Biso mean: 58.22 Å2 / Biso min: 32.89 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.038
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Xplor file |
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