+Open data
-Basic information
Entry | Database: PDB / ID: 2zw0 | ||||||
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Title | Crystal structure of a Streptococcal protein G B1 mutant | ||||||
Components | Protein LG | ||||||
Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN BINDING DOMAIN / PH-DEPENDENT LIGAND BINDING | ||||||
Function / homology | Protein L, Ig light chain-binding / Protein L b1 domain / IgG-binding B / B domain / Ubiquitin-like (UB roll) - #10 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / Protein LG Function and homology information | ||||||
Biological species | Finegoldia magna (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Watanabe, H. / Matsumaru, H. / Odahara, T. / Suto, K. / Honda, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Optimizing pH response of affinity between protein G and IgG Fc: how electrostatic modulations affect protein-protein interactions. Authors: Watanabe, H. / Matsumaru, H. / Ooishi, A. / Feng, Y. / Odahara, T. / Suto, K. / Honda, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zw0.cif.gz | 25.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zw0.ent.gz | 16 KB | Display | PDB format |
PDBx/mmJSON format | 2zw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/2zw0 ftp://data.pdbj.org/pub/pdb/validation_reports/zw/2zw0 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6395.004 Da / Num. of mol.: 1 / Fragment: B1 domain / Mutation: D36E, N37H, D47P, A48E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Finegoldia magna (bacteria) / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53291 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.72 Å3/Da / Density % sol: 28.3 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 24, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 9052 / Redundancy: 6.5 % / Biso Wilson estimate: 11.346 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.1 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.012 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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