[English] 日本語
![](img/lk-miru.gif)
- PDB-1h4a: Human GammaD Crystallin R58H mutant structure AT 1.15 A resolution -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1h4a | ||||||
---|---|---|---|---|---|---|---|
Title | Human GammaD Crystallin R58H mutant structure AT 1.15 A resolution | ||||||
![]() | Gamma-crystallin D | ||||||
![]() | EYE LENS PROTEIN / CRYSTALLIN | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Basak, A.K. / Slingsby, C. | ||||||
![]() | ![]() 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. #2: Journal: Proteins: Struct.,Funct., Genet. / Year: 1988 Title: Surface Interactions of Gamma-Crystallins in the Crystal Medium in Relation to Their Association in the Eye Lens Authors: Sergeev, Y.V. / Chirgadze, Y.N. / Mylvaganam, S.E. / Driessen, H. / Slingsby, C. / Blundell, T.L. #3: Journal: Mol.Biol.(Engl.Transl.) / Year: 1987 Title: Key Role of Residue 103 in Surface Interactions of Gamma-Crystallins Authors: Sergeev Yu, V. / Chirgadze Yu, N. / Driessen, H. / Slingsby, C. / Blundell, T.L. #4: ![]() Title: Phase Improvement in Protein Crystallography Using a Mixed Electron Density Model Authors: Lunin Yu, V. / Urzhumtsev, A.G. / Vernoslova, E.A. / Chirgadze Yu, N. / Nevskaya, N.A. / Fomenkova, N.P. #5: Journal: J.Mol.Biol. / Year: 1977 Title: Crystallographic Study of Gamma-Crystallins from Calf Lens Authors: Chirgadze, Y.N. / Nikonov, S.V. / Garber, M.B. / Reshetnikova, L.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 95.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 72.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 427.4 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hk0C ![]() 1elpS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 20615.922 Da / Num. of mol.: 1 / Mutation: R58H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
Compound details | DOMINANT STRUCTURAL COMPONENTS OF THE VERTEBRATE EYE LENS. THESE PROTEINS HAVE A TWO-DOMAIN BETA- ...DOMINANT STRUCTURAL |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 39 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2001 / Details: MIRROR |
Radiation | Monochromator: LAUE DIAMOND C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→28.33 Å / Num. obs: 55087 / % possible obs: 95.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.15→1.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 6.3 / % possible all: 97.6 |
Reflection | *PLUS Num. measured all: 463412 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 97.6 % |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ELP Resolution: 1.15→27.02 Å / SU B: 0.504 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.041 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||
Displacement parameters | Biso mean: 8.566 Å2
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→27.02 Å
| ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 28.33 Å / % reflection Rfree: 8 % / Rfactor obs: 0.1576 / Rfactor Rfree: 0.1822 / Rfactor Rwork: 0.1555 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
|