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Yorodumi- PDB-6nl6: Crystal structure of mutant B1 immunoglobulin-binding domain of S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nl6 | ||||||
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Title | Crystal structure of mutant B1 immunoglobulin-binding domain of Streptococcal Protein G (T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, N35K, D36H, N37Q) | ||||||
Components | Immunoglobulin G-binding protein G | ||||||
Keywords | DE NOVO PROTEIN / Metal-mediated complex / 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: 1.4 Å | ||||||
Authors | Huxford, T. / Stec, B. / Maniaci, B. | ||||||
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 | 6nl6.cif.gz | 123.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nl6.ent.gz | 94.9 KB | Display | PDB format |
PDBx/mmJSON format | 6nl6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nl6_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 6nl6_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 6nl6_validation.xml.gz | 18 KB | Display | |
Data in CIF | 6nl6_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/6nl6 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/6nl6 | HTTPS FTP |
-Related structure data
Related structure data | 6nl7C 6nl8C 6nl9C 6nlaC 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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Unit cell |
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-Components
#1: Antibody | Mass: 6348.063 Da / Num. of mol.: 4 Mutation: T16F, T18A, V21E, T25L, K28Y, V29I, K31R, Q32H, Y33L, D36H, N35K, D36A, N37Q 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): BL21DE3 / References: UniProt: P19909 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: 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: 2.21 Å3/Da / Density % sol: 44.33 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 70 mM acetic Acid pH 3.6, 30 mM acetic acid pH 5.8, 30% 2,4-methylpentanediol, 100 mM NaCl, and 20 mM zinc sulfate PH range: 3.6 - 5.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.00002 Å | |||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 15, 2012 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.4→37.38 Å / Num. obs: 42380 / % possible obs: 95.7 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.8 | |||||||||||||||
Reflection shell | Resolution: 1.4→1.44 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.29 / Num. unique obs: 2092 / % possible all: 70.44 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PGA Resolution: 1.4→37.38 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.131 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.015 / 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: 17.271 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→37.38 Å
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Refine LS restraints |
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