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Yorodumi- PDB-6nla: Crystal structure of de novo designed metal-controlled dimer of B... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nla | ||||||
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Title | Crystal structure of de novo designed metal-controlled dimer of B1 immunoglobulin-binding domain of Streptococcal Protein G (L12H, E15V, T16L, T18I, V29H, Y33H, N37L)-zinc | ||||||
Components | Immunoglobulin G-binding protein G | ||||||
Keywords | DE NOVO PROTEIN / Metal-mediated dimer / B1 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: 1.34 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nla.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nla.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 6nla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nla_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
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Full document | 6nla_full_validation.pdf.gz | 434.6 KB | Display | |
Data in XML | 6nla_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 6nla_validation.cif.gz | 8.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/6nla ftp://data.pdbj.org/pub/pdb/validation_reports/nl/6nla | HTTPS FTP |
-Related structure data
Related structure data | 6nl6C 6nl7C 6nl8C 6nl9C 6nlbC 1pgaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Antibody , 1 types, 1 molecules A
#1: Antibody | Mass: 6233.942 Da / Num. of mol.: 1 / Mutation: L12H, E15V, T16L, T18I, 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 |
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-Non-polymers , 5 types, 121 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 4M NaCl 0.1M HEPES pH 7.5 50mM MgCl2, 5mM zinc sulfate PH range: 7.3-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: 1.34→31.58 Å / Num. obs: 16453 / % possible obs: 97.95 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.34→1.374 Å / Num. unique obs: 1038 / % possible all: 83.64 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PGA Resolution: 1.34→31.58 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.943 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.034 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.219 Å2
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Refinement step | Cycle: 1 / Resolution: 1.34→31.58 Å
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Refine LS restraints |
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