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Yorodumi- PDB-2o6q: Structural diversity of the hagfish Variable Lymphocyte Receptors A29 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o6q | ||||||
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Title | Structural diversity of the hagfish Variable Lymphocyte Receptors A29 | ||||||
Components | Variable lymphocyte receptor A | ||||||
Keywords | IMMUNE SYSTEM / Leucine-rich repeat protein / LRR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Eptatretus burgeri (inshore hagfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Lee, J.O. / Kim, H.M. / Oh, S.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Structural diversity of the hagfish variable lymphocyte receptors Authors: Kim, H.M. / Oh, S.C. / Lim, K.J. / Kasamatsu, J. / Heo, J.Y. / Park, B.S. / Lee, H. / Yoo, O.J. / Kasahara, M. / Lee, J.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o6q.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o6q.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 2o6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/2o6q ftp://data.pdbj.org/pub/pdb/validation_reports/o6/2o6q | HTTPS FTP |
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-Related structure data
Related structure data | 2o6rC 2o6sC 1oznS C: citing same article (ref.) 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: Protein | Mass: 30137.842 Da / Num. of mol.: 1 / Fragment: Leucine-rich repeat (LRR), residues 23-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eptatretus burgeri (inshore hagfish) / Gene: VLRA / Plasmid: pVL1393 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q32R26 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 33% PEG 1000, 0.1M Bis-Tris, 0.2M magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97175 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 9, 2006 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97175 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 14364 / Num. obs: 13115 / % possible obs: 91 % / Redundancy: 4.9 % / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.09 / Net I/σ(I): 17.4 |
Reflection shell | Highest resolution: 2.5 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.287 / % possible all: 61.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1OZN Resolution: 2.5→19.93 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 274429.95 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.4322 Å2 / ksol: 0.303326 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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