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Open data
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Basic information
Entry | Database: PDB / ID: 5d1q | ||||||
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Title | IsdB NEAT2 bound by clone D2-06 | ||||||
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Function / homology | ![]() heme transmembrane transporter activity / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Deng, X. | ||||||
![]() | ![]() Title: Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire. Authors: Yeung, Y.A. / Foletti, D. / Deng, X. / Abdiche, Y. / Strop, P. / Glanville, J. / Pitts, S. / Lindquist, K. / Sundar, P.D. / Sirota, M. / Hasa-Moreno, A. / Pham, A. / Melton Witt, J. / Ni, I. ...Authors: Yeung, Y.A. / Foletti, D. / Deng, X. / Abdiche, Y. / Strop, P. / Glanville, J. / Pitts, S. / Lindquist, K. / Sundar, P.D. / Sirota, M. / Hasa-Moreno, A. / Pham, A. / Melton Witt, J. / Ni, I. / Pons, J. / Shelton, D. / Rajpal, A. / Chaparro-Riggers, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 388.7 KB | Display | ![]() |
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PDB format | ![]() | 329.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23386.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Cloned from B Cells / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 27782.600 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Antibody | Mass: 29434.365 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#4: Antibody | Mass: 23564.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Protein | Mass: 14034.010 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: bovine RF122 / ET3-1 / Gene: isdB, frpB, sasJ, sirH, SAB0993c / Production host: ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.35 % / Description: Plates |
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Crystal grow![]() | Temperature: 293 K / Method: microbatch / Details: 20% PEG3350 0.1M Na Citrate pH 5.4 / PH range: 5.5-6 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.22→47.33 Å / Num. obs: 22680 / % possible obs: 98.8 % / Redundancy: 6.6 % / Net I/σ(I): 20.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 72.971 Å2
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Refinement step | Cycle: LAST / Resolution: 3.22→47.33 Å
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Refine LS restraints |
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