+Open data
-Basic information
Entry | Database: PDB / ID: 1hk0 | ||||||
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Title | Human GammaD Crystallin Structure at 1.25 A Resolution | ||||||
Components | Gamma-crystallin D | ||||||
Keywords | EYE LENS PROTEIN / CATARACT | ||||||
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: 1.25 Å | ||||||
Authors | Basak, A.K. / Slingsby, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: High-Resolution X-Ray Crystal Structures of Human Gammad Crystallin (1.25A) and the R58H Mutant (1.15A) Associated with Aculeiform Cataract Authors: Basak, A.K. / Bateman, O. / Slingsby, C. / Pande, A. / Asherie, N. / Ogun, O. / Benedek, G. / Pande, J. #1: Journal: Exp.Eye Res. / Year: 1991 Title: Crystal Structure of Calf Eye Lens Gamma-Crystallin Iiib at 2.5 A Resolution: Its Relation to Function Authors: Yu, C. / Nevskaya, N. / Vernoslova, E. / Nikonov, S. / Yu, S. / Brazhnikov, E. / Fomenkova, N. / Lunin, V. / Urzhumtsev, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hk0.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hk0.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 1hk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/1hk0 ftp://data.pdbj.org/pub/pdb/validation_reports/hk/1hk0 | HTTPS FTP |
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-Related structure data
Related structure data | 1h4aC 1elpS 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: 20634.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CRYGD, CRYG4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / 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: 1.87 Å3/Da / Density % sol: 38 % | ||||||||||||||||||
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Crystal grow | Temperature: 277 K / pH: 7 / Details: 10MM PHOSPHATE, 4 DEGREE CELSIUS, pH 7.00 | ||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: batch method | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 2001 / Details: MIRROR |
Radiation | Monochromator: LAUE DIAMOND C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→28.17 Å / Num. obs: 39066 / % possible obs: 86.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.25→1.32 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3.7 / % possible all: 45.5 |
Reflection | *PLUS Num. obs: 39021 / Num. measured all: 212732 |
Reflection shell | *PLUS % possible obs: 45.5 % / Redundancy: 1.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ELP Resolution: 1.25→28.17 Å / SU B: 0.877 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.062 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 13.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→28.17 Å
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Refinement | *PLUS % reflection Rfree: 8 % / Rfactor obs: 0.1671 / Rfactor Rfree: 0.2078 / Rfactor Rwork: 0.1636 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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