+Open data
-Basic information
Entry | Database: PDB / ID: 6w5b | ||||||
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Title | N124D Deamidation Mutant of Human gammaD-Crystallin | ||||||
Components | Gamma-crystallin D | ||||||
Keywords | STRUCTURAL PROTEIN / deamidation / lens / cataract / protein modification | ||||||
Function / homology | Function and homology information lens fiber cell differentiation / structural constituent of eye lens / lens development in camera-type eye / visual perception / cellular response to reactive oxygen species / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Whitley, M.J. / Rathi, N. / Ambarian, M. / Gronenborn, A.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2021 Title: Assessing the Structures and Interactions of gamma D-Crystallin Deamidation Variants. Authors: Guseman, A.J. / Whitley, M.J. / Gonzalez, J.J. / Rathi, N. / Ambarian, M. / Gronenborn, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w5b.cif.gz | 120.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w5b.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 6w5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/6w5b ftp://data.pdbj.org/pub/pdb/validation_reports/w5/6w5b | HTTPS FTP |
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-Related structure data
Related structure data | 6wcyC 1hk0S S: Starting model for refinement C: citing same article (ref.) |
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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: 20635.955 Da / Num. of mol.: 1 / Mutation: N125D Source method: isolated from a genetically manipulated source Details: No electron density for the last three residues. / Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P07320 |
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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: 1.97 Å3/Da / Density % sol: 37.53 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→28.17 Å / Num. obs: 58473 / % possible obs: 99.32 % / Redundancy: 11.6 % / Biso Wilson estimate: 12.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.02 / Rrim(I) all: 0.071 / Net I/σ(I): 17.43 |
Reflection shell | Resolution: 1.15→1.191 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5481 / CC1/2: 0.866 / Rpim(I) all: 0.2414 / Rrim(I) all: 0.5748 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HK0 Resolution: 1.15→28.17 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.14 Details: Anisotropic ADPs refined for all non-hydrogen protein atoms. Explicit riding hydrogens added to model for refinement.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→28.17 Å
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Refine LS restraints |
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LS refinement shell |
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