+Open data
-Basic information
Entry | Database: PDB / ID: 1ytq | ||||||
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Title | Structure of Native Human Beta B2 Crystallin | ||||||
Components | Beta crystallin B2 | ||||||
Keywords | STRUCTURAL PROTEIN / Crystallin / Domain Swapping / greek key | ||||||
Function / homology | Function and homology information structural constituent of eye lens / lens development in camera-type eye / response to stimulus / visual perception / structural molecule activity / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Slingsby, C. / Smith, M.A. / Bateman, O.A. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Mutation of interfaces in domain-swapped human betaB2-crystallin Authors: Smith, M.A. / Bateman, O.A. / Jaenicke, R. / Slingsby, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ytq.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ytq.ent.gz | 38.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ytq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/1ytq ftp://data.pdbj.org/pub/pdb/validation_reports/yt/1ytq | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23280.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRYBB2 / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P43320 |
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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: 3.67 Å3/Da / Density % sol: 66.5 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8 Details: MPD, cacodylate, DTT, magnesium chloride, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 11, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→34.4 Å / Num. all: 36271 / Num. obs: 35758 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.7→34.4 Å / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.311 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.388 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→34.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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