[English] 日本語
Yorodumi- PDB-8cqo: Crystal structure of Borrelia burgdorferi paralogous family 12 ou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cqo | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Borrelia burgdorferi paralogous family 12 outer surface protein BBK01 (Se-Met data) | ||||||
Components | Lipoprotein, putative | ||||||
Keywords | DNA BINDING PROTEIN / paralogous protein / PFam12 | ||||||
Function / homology | Prokaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein, putative Function and homology information | ||||||
Biological species | Borreliella burgdorferi B31 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å | ||||||
Authors | Brangulis, K. / Drunka, L. / Matisone, S. / Akopjana, I. / Tars, K. | ||||||
Funding support | Latvia, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of Borrelia burgdorferi outer surface protein BBK01 Authors: Brangulis, K. / Drunka, L. / Matisone, S. / Akopjana, I. / Tars, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8cqo.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8cqo.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 8cqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cqo_validation.pdf.gz | 440.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8cqo_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 8cqo_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 8cqo_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/8cqo ftp://data.pdbj.org/pub/pdb/validation_reports/cq/8cqo | HTTPS FTP |
-Related structure data
Related structure data | 8cqnC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31880.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The first 4 residues (GAMG) are remnants from the expression tag. Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_K01 / Variant: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Plasmid: pETm-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50805 Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.47 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M Bicine pH 9.0 6% PEG 20 000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97965 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2022 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97965 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→47.49 Å / Num. obs: 7221 / % possible obs: 95.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3.3→3.56 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 6.3 / Num. unique obs: 1431 / % possible all: 94.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 3.3→47.49 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.887 / SU B: 19.862 / SU ML: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 162.16 Å2 / Biso mean: 59.789 Å2 / Biso min: 25.59 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.3→47.49 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.3→3.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|