+Open data
-Basic information
Entry | Database: PDB / ID: 3gbl | ||||||
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Title | Crystal structure of grass carp Beta2-microglobulin | ||||||
Components | Beta2-microglobulin | ||||||
Keywords | IMMUNE SYSTEM / Beta2-microglobulin / Immune response / Immunoglobulin domain / MHC I / Secreted | ||||||
Function / homology | Function and homology information antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / immune response / extracellular region Similarity search - Function | ||||||
Biological species | Ctenopharyngodon idella (grass carp) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Chen, W. / Gao, F. / Xia, C. / Gao, G.F. | ||||||
Citation | Journal: To be Published Title: Crystal structure of grass carp Beta2-microglobulin Authors: Chen, W. / Gao, F. / Xia, C. / Gao, G.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gbl.cif.gz | 36.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gbl.ent.gz | 24.2 KB | Display | PDB format |
PDBx/mmJSON format | 3gbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/3gbl ftp://data.pdbj.org/pub/pdb/validation_reports/gb/3gbl | HTTPS FTP |
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-Related structure data
Related structure data | 1ldsS 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: 11114.586 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-97 (UNIPROT 20-116) / Source method: isolated from a natural source / Source: (natural) Ctenopharyngodon idella (grass carp) / References: UniProt: Q65XZ7 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.1 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 6.5 Details: 0.1M MES pH 6.5, 12% PEG 20000, 3%(v/v) ethanol, EVAPORATION, temperature 291K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
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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→35.56 Å / Num. obs: 6986 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LDS Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.053 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.221 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.101→2.155 Å / Total num. of bins used: 20
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