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- PDB-1dee: Structure of S. aureus protein A bound to a human IgM Fab -

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Basic information

Entry
Database: PDB / ID: 1dee
TitleStructure of S. aureus protein A bound to a human IgM Fab
Components
  • (IGM RF 2A2) x 2
  • IMMUNOGLOBULIN G BINDING PROTEIN A
KeywordsIMMUNE 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


symbiont-mediated suppression of host signal transduction pathway via antagonism of host cell surface receptor / IgG binding / extracellular region
Similarity search - Function
Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsGraille, M. / Stura, E.A. / Corper, A.L. / Sutton, B.J. / Taussig, M.J. / Charbonnier, J.B. / Silverman, G.J.
CitationJournal: 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
DepositionNov 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGM RF 2A2
B: IGM RF 2A2
C: IGM RF 2A2
D: IGM RF 2A2
E: IGM RF 2A2
F: IGM RF 2A2
G: IMMUNOGLOBULIN G BINDING PROTEIN A
H: IMMUNOGLOBULIN G BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)154,7408
Polymers154,7408
Non-polymers00
Water18010
1
A: IGM RF 2A2
B: IGM RF 2A2


Theoretical massNumber of molelcules
Total (without water)47,5112
Polymers47,5112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-20 kcal/mol
Surface area19040 Å2
MethodPISA
2
C: IGM RF 2A2
D: IGM RF 2A2
G: IMMUNOGLOBULIN G BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)53,6153
Polymers53,6153
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: IGM RF 2A2
F: IGM RF 2A2
H: IMMUNOGLOBULIN G BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)53,6153
Polymers53,6153
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: IGM RF 2A2
F: IGM RF 2A2


Theoretical massNumber of molelcules
Total (without water)47,5112
Polymers47,5112
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-19 kcal/mol
Surface area19040 Å2
MethodPISA
5
C: IGM RF 2A2
D: IGM RF 2A2


Theoretical massNumber of molelcules
Total (without water)47,5112
Polymers47,5112
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-19 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.520, 78.910, 163.240
Angle α, β, γ (deg.)90.00, 100.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody IGM RF 2A2


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 IGM RF 2A2


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 IMMUNOGLOBULIN G BINDING PROTEIN A


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 / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
221-24 %(w/w)mPEG50001reservoir
3100 mMsodium cacodylate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceTypeIDWavelength
ROTATING ANODERIGAKU11.5418
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJul 4, 1998
MARRESEARCH2IMAGE PLATEDec 28, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 184708 / Num. obs: 46831 / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.065
Reflection shellResolution: 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

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementResolution: 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.
RfactorNum. reflectionSelection details
Rfree0.281 2328 RANDOM
Rwork0.217 --
all0.225 46742 -
obs0.225 44414 -
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10849 0 0 10 10859
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.59

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