[English] 日本語
Yorodumi- PDB-3q69: X-ray crystal structure of a MucBP domain of the protein LBA1460 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q69 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of a MucBP domain of the protein LBA1460 from Lactobacillus acidophilus, Northeast structural genomics consortium target LaR80A | ||||||
Components | probable Zn binding protein | ||||||
Keywords | METAL BINDING PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / domain family PF06458 | ||||||
Function / homology | Immunoglobulin-like - #4300 / Mub B2-like domain / Muc B2-like domain / Immunoglobulin-like / Sandwich / Mainly Beta / Putative mucus binding protein Function and homology information | ||||||
Biological species | Lactobacillus acidophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å | ||||||
Authors | Seetharaman, J. / Lew, S. / Forouhar, F. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. ...Seetharaman, J. / Lew, S. / Forouhar, F. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: X-ray crystal structure of a MucBP domain of the protein LBA1460 from Lactobacillus acidophilus, Northeast structural genomics consortium target LaR80A Authors: Seetharaman, J. / Lew, S. / Forouhar, F. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3q69.cif.gz | 31 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3q69.ent.gz | 23 KB | Display | PDB format |
PDBx/mmJSON format | 3q69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q69_validation.pdf.gz | 400.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3q69_full_validation.pdf.gz | 401.5 KB | Display | |
Data in XML | 3q69_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 3q69_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/3q69 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/3q69 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14093.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: LBA1460 / References: UniProt: Q5FJ43 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.88 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 3350, .1M KBr .1M Bis Tris Propane pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 11754 / Num. obs: 9462 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.063 |
Reflection shell | Resolution: 2.4→2.44 Å / % possible all: 94.6 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.4→29.29 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 937353.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.5739 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 25.4 Å2
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→29.29 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
| ||||||||||||||||||||
Xplor file |
|