[English] 日本語
Yorodumi- PDB-7bkx: Diploptera punctata inspired lipocalin-like Milk protein expresse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bkx | ||||||
---|---|---|---|---|---|---|---|
Title | Diploptera punctata inspired lipocalin-like Milk protein expressed in Saccharomyces cerevisiae | ||||||
Components | Milk protein | ||||||
Keywords | LIPID BINDING PROTEIN / Lipocalin-like protein / Milk protein / Beta-barrel / N-glycosylation | ||||||
Function / homology | Calycin / metal ion binding / PALMITOLEIC ACID / Milk protein Function and homology information | ||||||
Biological species | Diploptera punctata (Pacific beetle cockroach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Banerjee, S. / Kanagavijayan, D. / Subramanian, R. / Santhakumari, P.R. / Chavas, L.M.G. / Ramaswamy, S. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Biochim Biophys Acta Gen Subj / Year: 2022 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. / Banerjee, S. #1: Journal: IUCrJ / Year: 2016 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7bkx.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7bkx.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7bkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bkx_validation.pdf.gz | 932.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7bkx_full_validation.pdf.gz | 940.2 KB | Display | |
Data in XML | 7bkx_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 7bkx_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/7bkx ftp://data.pdbj.org/pub/pdb/validation_reports/bk/7bkx | HTTPS FTP |
-Related structure data
Related structure data | 7q02C 4nyqS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 20637.365 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Diploptera punctata (Pacific beetle cockroach) Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q6SVB5 |
---|
-Sugars , 2 types, 4 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#3: Sugar |
-Non-polymers , 4 types, 31 molecules
#4: Chemical | ChemComp-PAM / | ||
---|---|---|---|
#5: Chemical | ChemComp-GOL / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.43 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 15% of PEG MME 550, 100 mM MES pH 6.5, and 10 mM ZnSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→20.612 Å / Num. obs: 12200 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rrim(I) all: 0.073 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.35→2.39 Å / Num. unique obs: 1224 / CC1/2: 0.3 / Rrim(I) all: 0.836 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NYQ Resolution: 2.35→20.6 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 18.065 / SU ML: 0.207 / Cross valid method: FREE R-VALUE / ESU R: 0.251 / ESU R Free: 0.228 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: 58.393 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→20.6 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 3.1056 Å / Origin y: 21.3104 Å / Origin z: 17.965 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection: ALL |