[English] 日本語
Yorodumi- PDB-6nl9: Crystal structure of de novo designed metal-controlled dimer of m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nl9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of de novo designed metal-controlled dimer of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, T16L, V29H, Y33H, N37L)-apo | ||||||
Components | Immunoglobulin G-binding protein G | ||||||
Keywords | DE NOVO PROTEIN / Metal-mediated complex / Beta1 Domain of Streptococcal protein G / Immunoglobulin binding protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Maniaci, B. / Stec, B. / Huxford, T. | ||||||
Citation | Journal: Biochemistry / Year: 2019 Title: Design of High-Affinity Metal-Controlled Protein Dimers. Authors: Maniaci, B. / Lipper, C.H. / Anipindi, D.L. / Erlandsen, H. / Cole, J.L. / Stec, B. / Huxford, T. / Love, J.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6nl9.cif.gz | 61.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6nl9.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 6nl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nl9_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6nl9_full_validation.pdf.gz | 444.1 KB | Display | |
Data in XML | 6nl9_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 6nl9_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/6nl9 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/6nl9 | HTTPS FTP |
-Related structure data
Related structure data | 6nl6C 6nl7C 6nl8C 6nlaC 6nlbC 1pgaS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 6251.871 Da / Num. of mol.: 4 / Mutation: L12H, T16L, V29H, Y33H, N37L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus (bacteria) / Gene: spg / Plasmid: pET21a / Details (production host): T7 expression / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19909 #2: Chemical | ChemComp-MG / | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.45 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 4000 0.1M HEPES pH 7.5 200 mM MgCl2 / PH range: 7.3-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.0083 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0083 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45.64 Å / Num. obs: 21921 / % possible obs: 96.7 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.7→1.74 Å / Num. unique obs: 1276 / % possible all: 76.28 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PGA Resolution: 1.7→45.64 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.941 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.566 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.7→45.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|