+Open data
-Basic information
Entry | Database: PDB / ID: 5d1x | ||||||
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Title | IsdB NEAT2 bound by D4-30 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IsdB / NEAT2 / germline encoded | ||||||
Function / homology | Function and homology information heme transmembrane transporter activity / cell wall / : / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å | ||||||
Authors | Deng, X. | ||||||
Citation | Journal: Nat Commun / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d1x.cif.gz | 178.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d1x.ent.gz | 144.1 KB | Display | PDB format |
PDBx/mmJSON format | 5d1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d1x_validation.pdf.gz | 462.2 KB | Display | wwPDB validaton report |
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Full document | 5d1x_full_validation.pdf.gz | 482.6 KB | Display | |
Data in XML | 5d1x_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 5d1x_validation.cif.gz | 44.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/5d1x ftp://data.pdbj.org/pub/pdb/validation_reports/d1/5d1x | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24085.846 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 27757.658 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#3: Antibody | Mass: 29434.365 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#4: Antibody | Mass: 23651.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
#5: Protein | Mass: 13879.844 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria) Strain: USA300 / Gene: isdB, frpB, sasJ, sirH, SAUSA300_1028 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q2FHV2, UniProt: Q2FZF0*PLUS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.67 % |
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Crystal grow | Temperature: 290 K / Method: microbatch / Details: 15% PEG10k 0.1M Tris pH 8 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.987 Å |
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: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3.21→49.79 Å / % possible obs: 99 % / Redundancy: 3.6 % / Net I/σ(I): 9.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→49.18 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.887 / SU B: 74.469 / SU ML: 0.545 / Cross valid method: THROUGHOUT / ESU R Free: 0.594 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: 87.022 Å2
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Refinement step | Cycle: LAST / Resolution: 3.21→49.18 Å
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Refine LS restraints |
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