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- PDB-9m6o: Crystal structure of S. aureus protein A bound to a camelid singl... -

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Basic information

Entry
Database: PDB / ID: 9m6o
TitleCrystal structure of S. aureus protein A bound to a camelid single-domain antibody
Components
  • Immunoglobulin G-binding protein A
  • single-domain antibody
KeywordsIMMUNE SYSTEM / Complex
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
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 ...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
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsKong, Y. / Shi, J.L. / Wu, F.D. / Zhao, T. / Zhu, X.Y. / Xu, Q.Y. / Wang, R.B. / Song, Y.D. / Li, Q.X. / Wang, Y.L. ...Kong, Y. / Shi, J.L. / Wu, F.D. / Zhao, T. / Zhu, X.Y. / Xu, Q.Y. / Wang, R.B. / Song, Y.D. / Li, Q.X. / Wang, Y.L. / Gao, X.Y. / Yang, Y.D. / Wu, Y.L. / Yang, Z.L. / Yao, J.H. / Ying, T.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82394450 China
CitationJournal: Cell Discov / Year: 2025
Title: A synergistic generative-ranking framework for tailored design of therapeutic single-domain antibodies.
Authors: Kong, Y. / Shi, J. / Wu, F. / Zhao, T. / Wang, R. / Zhu, X. / Xu, Q. / Song, Y. / Li, Q. / Wang, Y. / Gao, X. / Yang, Y. / Feng, Y. / Wang, Z. / Ge, W. / Wu, Y. / Yang, Z. / Yao, J. / Ying, T.
History
DepositionMar 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Immunoglobulin G-binding protein A
A: Immunoglobulin G-binding protein A
B: single-domain antibody
C: single-domain antibody


Theoretical massNumber of molelcules
Total (without water)41,5944
Polymers41,5944
Non-polymers00
Water6,323351
1
H: Immunoglobulin G-binding protein A
C: single-domain antibody


Theoretical massNumber of molelcules
Total (without water)20,7972
Polymers20,7972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-4 kcal/mol
Surface area9020 Å2
MethodPISA
2
A: Immunoglobulin G-binding protein A
B: single-domain antibody


Theoretical massNumber of molelcules
Total (without water)20,7972
Polymers20,7972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-4 kcal/mol
Surface area9030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.930, 78.480, 97.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A / SpA


Mass: 6845.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Gene: spa, SAOUHSC_00069 / Production host: Escherichia coli (E. coli) / References: UniProt: P02976
#2: Antibody single-domain antibody


Mass: 13951.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% w/v Polyethylene glycol 3350 and 0.1M Citric acid 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.49→29.98 Å / Num. obs: 66808 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 15.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Net I/σ(I): 10.5
Reflection shellResolution: 1.49→1.53 Å / Rmerge(I) obs: 1.316 / Num. unique obs: 4852 / CC1/2: 0.768

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286phasing
PHENIX1.21.1_5286refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→29.94 Å / SU ML: 0.1618 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 46.1208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2565 3250 4.88 %
Rwork0.2244 63287 -
obs0.2259 66537 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.32 Å2
Refinement stepCycle: LAST / Resolution: 1.49→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 0 351 3151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00882852
X-RAY DIFFRACTIONf_angle_d1.0253858
X-RAY DIFFRACTIONf_chiral_restr0.0852408
X-RAY DIFFRACTIONf_plane_restr0.0079516
X-RAY DIFFRACTIONf_dihedral_angle_d13.33531046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.51151220.4342721X-RAY DIFFRACTION98.92
1.51-1.540.44011310.41762709X-RAY DIFFRACTION99.61
1.54-1.560.39851310.38642736X-RAY DIFFRACTION99.55
1.56-1.590.33491580.37052698X-RAY DIFFRACTION99.69
1.59-1.620.38641180.35972744X-RAY DIFFRACTION99.86
1.62-1.650.34261520.33552723X-RAY DIFFRACTION99.79
1.65-1.680.36611300.32352697X-RAY DIFFRACTION99.44
1.68-1.720.37621550.31162733X-RAY DIFFRACTION99.65
1.72-1.760.27511450.2932749X-RAY DIFFRACTION99.48
1.76-1.80.32011420.27312702X-RAY DIFFRACTION99.68
1.8-1.850.32041280.26312742X-RAY DIFFRACTION99.86
1.85-1.910.25241330.24572775X-RAY DIFFRACTION99.79
1.91-1.970.26721330.23722737X-RAY DIFFRACTION99.48
1.97-2.040.2441430.222715X-RAY DIFFRACTION99.55
2.04-2.120.25711420.20222770X-RAY DIFFRACTION99.66
2.12-2.210.2161370.19412760X-RAY DIFFRACTION99.9
2.21-2.330.22691470.18642728X-RAY DIFFRACTION99.83
2.33-2.480.22911810.1952735X-RAY DIFFRACTION99.79
2.48-2.670.211480.18772777X-RAY DIFFRACTION99.9
2.67-2.940.19831330.18372803X-RAY DIFFRACTION99.53
2.94-3.360.2381300.17992820X-RAY DIFFRACTION99.9
3.36-4.230.21671450.17182846X-RAY DIFFRACTION100
4.23-29.940.21841660.19292867X-RAY DIFFRACTION96.93

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