+Open data
-Basic information
Entry | Database: PDB / ID: 1dee | ||||||
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Title | Structure of S. aureus protein A bound to a human IgM Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM / FAB-IBP COMPLEX CRYSTAL STRUCTURE 2.7A RESOLUTION BINDING OUTSIDE THE ANTIGEN COMBINING SITE SUPERANTIGEN FAB VH3 SPECIFICITY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.7 Å | ||||||
Authors | Graille, M. / Stura, E.A. / Corper, A.L. / Sutton, B.J. / Taussig, M.J. / Charbonnier, J.B. / Silverman, G.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity. Authors: Graille, M. / Stura, E.A. / Corper, A.L. / Sutton, B.J. / Taussig, M.J. / Charbonnier, J.B. / Silverman, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dee.cif.gz | 273.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dee.ent.gz | 226.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dee_validation.pdf.gz | 485.2 KB | Display | wwPDB validaton report |
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Full document | 1dee_full_validation.pdf.gz | 520.3 KB | Display | |
Data in XML | 1dee_validation.xml.gz | 50.4 KB | Display | |
Data in CIF | 1dee_validation.cif.gz | 68.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/1dee ftp://data.pdbj.org/pub/pdb/validation_reports/de/1dee | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23343.846 Da / Num. of mol.: 3 / Fragment: FAB LIGHT CHAIN / Source method: isolated from a natural source Details: FAB OF THE V3-30/ VH1.9III-ENCODED 2A2 IGM RHEUMATOID FACTOR PRODUCED BY TRYPSIN CLEAVAGE OF THE IGM SECRETED BY A HYBRIDOMA CREATED FROM SYNOVIAL B CELLS OF A RHEUMATOID ARTHRITIS PATIENT Source: (natural) Homo sapiens (human) #2: Antibody | Mass: 24167.008 Da / Num. of mol.: 3 / Fragment: FAB HEAVY CHAIN / Source method: isolated from a natural source Details: FAB OF THE V3-30/ VH1.9III-ENCODED 2A2 IGM RHEUMATOID FACTOR PRODUCED BY TRYPSIN CLEAVAGE OF THE IGM SECRETED BY A HYBRIDOMA CREATED FROM SYNOVIAL B CELLS OF A RHEUMATOID ARTHRITIS PATIENT Source: (natural) Homo sapiens (human) #3: Antibody | Mass: 6103.695 Da / Num. of mol.: 2 / Fragment: RECOMBINANT DOMAIN D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Staphylococcus aureus (bacteria) / References: UniProt: P02976 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.09 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MPEG 5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.7→20 Å / Num. all: 184708 / Num. obs: 46831 / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.065 | |||||||||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.37 / % possible all: 77 | |||||||||||||||
Reflection | *PLUS % possible obs: 87 % | |||||||||||||||
Reflection shell | *PLUS % possible obs: 77 % / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Resolution: 2.7→10 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: The 3 amino acids at the N terminus (FNK) of chain G have been removed for the refinement as they did not fit in any electronic density. However, the same amino acids have been kept in chain ...Details: The 3 amino acids at the N terminus (FNK) of chain G have been removed for the refinement as they did not fit in any electronic density. However, the same amino acids have been kept in chain H for refinement as more electron density is observed. The side chain atoms of Lys 805 from chain H are not defined by electronic density, then we decided to remove these atoms.
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Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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