+
Open data
-
Basic information
Entry | Database: PDB / ID: 8f0v | ||||||
---|---|---|---|---|---|---|---|
Title | Lipocalin-like Milk protein-2 - E38A mutant | ||||||
![]() | Milk protein | ||||||
![]() | LIPID BINDING PROTEIN / Lipocalin / Mutation / cockroach milk / Lili Mip. | ||||||
Function / homology | Calycin / metal ion binding / Milk protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Subramanian, R. / KanagaVijayan, D. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Variability in phenylalanine side chain conformations facilitates broad substrate tolerance of fatty acid binding in cockroach milk proteins. Authors: Santhakumari, P.R. / Dhanabalan, K. / Virani, S. / Hopf-Jannasch, A.S. / Benoit, J.B. / Chopra, G. / Subramanian, R. #1: ![]() Title: Structure of recombinantly expressed cockroach Lili-Mip protein in glycosylated and deglycosylated forms. Authors: KanagaVijayan, D. / Subramanian, R. / Santhakumari, P.R. / Chavas, L.M.G. / Subramanian, R. / Banerjee, S. #2: ![]() Title: Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata. Authors: Banerjee, S. / Coussens, N.P. / Gallat, F.X. / Sathyanarayanan, N. / Srikanth, J. / Yagi, K.J. / Gray, J.S. / Tobe, S.S. / Stay, B. / Chavas, L.M. / Ramaswamy, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 78.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 56.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 450 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f0yC ![]() 7bkxS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 17958.211 Da / Num. of mol.: 1 / Mutation: E38A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() | ||||||
---|---|---|---|---|---|---|---|
#2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 69 % / Description: diamond shaped crystals |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0 (0.002 M Zinc sulfate heptahydrate; 0.08 M HEPES pH 7.0; 25 % v/v Jeffamine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: May 7, 2022 / Details: double crystal |
Radiation | Monochromator: Rosenbaum-Rock monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→38.18 Å / Num. obs: 6461 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.054 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.95→3.13 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 1 / Num. unique obs: 1021 / CC1/2: 0.58 / Rpim(I) all: 0.83 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7BKX Resolution: 2.951→38.18 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.907 / SU B: 22.75 / SU ML: 0.376 / Cross valid method: THROUGHOUT / ESU R: 0.806 / ESU R Free: 0.404 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 98.323 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.951→38.18 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|