+Open data
-Basic information
Entry | Database: PDB / ID: 2xiw | ||||||
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Title | Crystal structure of the Sac7d-derived IgG1-binder C3-C24S | ||||||
Components | DNA-BINDING PROTEIN 7D | ||||||
Keywords | DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SULFOLOBUS ACIDOCALDARIUS (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Bellinzoni, M. / Colinet, S. / Behar, G. / Alzari, P.M. / Pecorari, F. | ||||||
Citation | Journal: Protein Eng.Des.Sel. / Year: 2013 Title: Tolerance of the Archaeal Sac7D Scaffold Protein to Alternative Library Designs: Characterization of Anti-Immunoglobulin G Affitins. Authors: Behar, G. / Bellinzoni, M. / Maillasson, M. / Paillard-Laurance, L. / Alzari, P.M. / He, X. / Mouratou, B. / Pecorari, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xiw.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xiw.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 2xiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/2xiw ftp://data.pdbj.org/pub/pdb/validation_reports/xi/2xiw | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.71044, 0.63121, 0.31122), Vector: |
-Components
#1: Protein | Mass: 9168.037 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS ACIDOCALDARIUS (acidophilic) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] / Variant (production host): IQ / References: UniProt: P13123 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Sequence details | N-TERMINAL STRETCH MRGSHHHHHH | |
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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: 2.92 Å3/Da / Density % sol: 57.9 % / Description: NONE |
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Crystal grow | Details: 3.5 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 19, 2009 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: CHANNEL CUT MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→31.7 Å / Num. obs: 28098 / % possible obs: 97.9 % / Observed criterion σ(I): 3 / Redundancy: 6.1 % / Biso Wilson estimate: 17.57 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.6 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.5→18.37 Å / Cor.coef. Fo:Fc: 0.9576 / Cor.coef. Fo:Fc free: 0.9524 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.065 / SU Rfree Cruickshank DPI: 0.062 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=1314. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=1314. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
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Displacement parameters | Biso mean: 22.93 Å2
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Refine analyze | Luzzati coordinate error obs: 0.182 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→18.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.56 Å / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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