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- PDB-9m6j: Crystal structure of S. aureus protein A bound to a camelid singl... -

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Basic information

Entry
Database: PDB / ID: 9m6j
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 speciesCamelidae (mammal)
Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
A: single-domain antibody
H: Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)20,8452
Polymers20,8452
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-4 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.580, 98.120, 52.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody single-domain antibody


Mass: 13999.470 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#2: Antibody Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A / SpA


Mass: 6845.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: spa, SAOUHSC_00069 / Production host: Escherichia coli (E. coli) / References: UniProt: P02976
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 49.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.0 M Ammonium sulfate

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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: Nov 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→61.34 Å / Num. obs: 13903 / % possible obs: 98.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 18.21 Å2 / CC1/2: 0.997 / Net I/σ(I): 37.1
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.117 / Num. unique obs: 981 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874phasing
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25.31 Å / SU ML: 0.1806 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.5807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2256 652 4.69 %
Rwork0.1924 13240 -
obs0.194 13892 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.18 Å2
Refinement stepCycle: LAST / Resolution: 2→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 0 153 1539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061413
X-RAY DIFFRACTIONf_angle_d0.77331911
X-RAY DIFFRACTIONf_chiral_restr0.0549202
X-RAY DIFFRACTIONf_plane_restr0.006253
X-RAY DIFFRACTIONf_dihedral_angle_d14.7676516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.150.21871270.19522557X-RAY DIFFRACTION96.86
2.15-2.370.21711260.19262594X-RAY DIFFRACTION98.34
2.37-2.710.23711350.20042644X-RAY DIFFRACTION98.93
2.71-3.420.23841430.20112649X-RAY DIFFRACTION99.15
3.42-25.310.21521210.18262796X-RAY DIFFRACTION99.18
Refinement TLS params.Method: refined / Origin x: 14.320227102442 Å / Origin y: 16.50178516662 Å / Origin z: 5.5587000582409 Å
111213212223313233
T0.11912892609865 Å2-0.0035078244887901 Å20.017904400238531 Å2-0.09736450080954 Å2-0.005972241653663 Å2--0.07611761764814 Å2
L3.3271186564683 °2-0.75801229724563 °20.10300115989096 °2-1.5345972172171 °20.28002879258727 °2--1.0593478228085 °2
S-0.016252440224346 Å °-0.052074398068025 Å °-0.017678126657747 Å °0.0036914539353877 Å °0.038731718221411 Å °-0.067821784689412 Å °-0.036530242127377 Å °0.055135949466764 Å °-0.019720067459713 Å °
Refinement TLS groupSelection details: all

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