+
Open data
-
Basic information
Entry | Database: PDB / ID: 1bd7 | ||||||
---|---|---|---|---|---|---|---|
Title | CIRCULARLY PERMUTED BB2-CRYSTALLIN | ||||||
![]() | CIRCULARLY PERMUTED BB2-CRYSTALLIN | ||||||
![]() | EYE-LENS PROTEIN / BETA-CRYSTALLIN B / MULTIGENE FAMILY | ||||||
Function / homology | ![]() structural constituent of eye lens / camera-type eye development / lens development in camera-type eye / visual perception / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wright, G. / Basak, A.K. / Mayr, E.-M. / Glockshuber, R. / Slingsby, C. | ||||||
![]() | ![]() Title: Circular permutation of betaB2-crystallin changes the hierarchy of domain assembly. Authors: Wright, G. / Basak, A.K. / Wieligmann, K. / Mayr, E.M. / Slingsby, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 81.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 61.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 440.9 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99112, 0.07111, -0.11239), Vector: |
-
Components
#1: Protein | Mass: 20153.424 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PROTEIN IN THE CRYSTAL LATTICE IS A DIMER / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 43 % / Description: TAKEN FROM WHOLE STRUCTURE | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.1 Details: PROTEIN CONCENTRATION 6 MGS/ML. 0.10 ML OF 0.5M MES-NAOH, PH 6.1, 0.51 ML OF 40% (W/V) PEG 8K, 0.10 ML OF 2M AMMONIUM ACETATE, 0.29 ML OF WATER, AT ROOM-TEMPERATURE. Temp details: room temp | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→26.88 Å / Num. obs: 7225 / % possible obs: 81.8 % / Redundancy: 1.9 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.78→2.88 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 7.7 / % possible all: 81.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: BB2 (C-TERMINAL DOMAIN) Resolution: 2.78→26.88 Å / Isotropic thermal model: RESTRAINT INDIVIDUALS / Cross valid method: THROUGHOUT Details: CIRCULAR PERMUTATION OF THE TWO DOMAIN DIMER OF BB2-CRYSTALLIN CONVERTS INTERMOLECULAR DOMAIN PAIRING INTO INTRAMOLECULAR PAIRING, PROMOTING A HIGHER LEVEL QUATERNARY ORGANISATION. PHE 173 ...Details: CIRCULAR PERMUTATION OF THE TWO DOMAIN DIMER OF BB2-CRYSTALLIN CONVERTS INTERMOLECULAR DOMAIN PAIRING INTO INTRAMOLECULAR PAIRING, PROMOTING A HIGHER LEVEL QUATERNARY ORGANISATION. PHE 173 COULD NOT BE MODELED IN THE ELECTRON DENSITY AND HAS BEEN EXCLUDED FROM BOTH SUBUNITS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 26.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.78→26.88 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev position: 0.136 Å / Weight position: 300 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.78→2.91 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|