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Yorodumi- PDB-3bj9: Crystal structure of the Surrogate Light Chain Variable Domain VpreBJ -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bj9 | ||||||
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Title | Crystal structure of the Surrogate Light Chain Variable Domain VpreBJ | ||||||
Components | Immunoglobulin iota chain, Immunoglobulin lambda-like polypeptide 1 | ||||||
Keywords | IMMUNE SYSTEM / immunoglobulin domain / beta sheet / Polymorphism | ||||||
Function / homology | Function and homology information Cell surface interactions at the vascular wall / immune response / endoplasmic reticulum / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Morstadt, L.M. / Bohm, A.A. / Stollar, B.D. / Baleja, J.D. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Engineering and characterization of a single chain surrogate light chain variable domain. Authors: Morstadt, L. / Bohm, A. / Yuksel, D. / Kumar, K. / Stollar, B.D. / Baleja, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bj9.cif.gz | 36.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bj9.ent.gz | 27.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/3bj9 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bj9 | 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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Components on special symmetry positions |
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-Components
#1: Antibody | Mass: 12937.543 Da / Num. of mol.: 1 Fragment: Fusion protein consists of Ig domain of VPREB protein and J-fragment of Ig lambda-5 Mutation: Ig domain of VpreB fused to J-segment of 14.1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPREB1, VPREB / Plasmid: pIg203 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)pLysE / References: UniProt: P12018 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE 14 RESIDUES: THVFGSGTQL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Imidazole, 1M Sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 |
Detector | Type: OXFORD / Detector: CCD / Date: Nov 30, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→55.73 Å / Num. all: 9774 / Num. obs: 9712 / % possible obs: 99.36 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 7.3 / % possible all: 92.38 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→15.97 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.895 / SU B: 3.25 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.819 Å2
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Refinement step | Cycle: LAST / Resolution: 2→15.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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