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- PDB-9njy: Terminal two domains of ClfA002 with bound Fab of AZD7745 -

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Basic information

Entry
Database: PDB / ID: 9njy
TitleTerminal two domains of ClfA002 with bound Fab of AZD7745
Components
  • Clumping factor A
  • Human antibody, heavy chain fragment, antigen binding
  • Human antibody, light chain, antigen binding
KeywordsIMMUNE SYSTEM / Staphylococcus Aureus / virulence factors / monoclonal antibody / prophylactic treatment
Function / homology
Function and homology information


cell adhesion / extracellular region
Similarity search - Function
: / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / YSIRK type signal peptide / Adhesion domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif ...: / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / YSIRK type signal peptide / Adhesion domain superfamily / 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
Biological speciesStaphylococcus aureus (bacteria)
Mammalia (mammals)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsOganesyan, V.Y.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Infect.Dis. / Year: 2025
Title: Structure of ClfA002 in complex with neutralizing antibody AZD7745 provides insight into its broad neutralization mechanism in Staphylococcus aureus infection.
Authors: Tkaczyk, C. / Keren-Kaplan, T. / Gamson, A. / Warrener, P. / Semenova, E. / Rosenthal, K. / Barnes, A. / Ahani, B. / Sellman, B.R. / Podlaha, O. / Oganesyan, V.
History
DepositionFeb 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clumping factor A
H: Human antibody, heavy chain fragment, antigen binding
L: Human antibody, light chain, antigen binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4965
Polymers80,3123
Non-polymers1842
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-35 kcal/mol
Surface area32550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.582, 66.164, 107.875
Angle α, β, γ (deg.)90.000, 90.583, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Clumping factor A / Fibrinogen receptor A / Fibrinogen-binding protein A


Mass: 33143.469 Da / Num. of mol.: 1 / Mutation: none
Source method: isolated from a genetically manipulated source
Details: Cell surface-associated protein implicated in virulence. Promotes bacterial attachment exclusively to the gamma-chain of human fibrinogen. Induces formation of bacterial clumps, which ...Details: Cell surface-associated protein implicated in virulence. Promotes bacterial attachment exclusively to the gamma-chain of human fibrinogen. Induces formation of bacterial clumps, which diminish the ability of group IIA phospholipase A2 to cause bacterial phospholipid hydrolysis and killing. Significantly decreases macrophage phagocytosis possibly thanks to the clumps, clumped bacteria being too large to be phagocytosed. Dominant factor responsible for human platelet aggregation, which may be an important mechanism for initiating infective endocarditis
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: N315 / Gene: clfA, SA0742 / Variant: 002 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q99VJ4
#2: Antibody Human antibody, heavy chain fragment, antigen binding


Mass: 23898.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalia (mammals) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Human antibody, light chain, antigen binding


Mass: 23269.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalia (mammals) / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.7 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7
Details: 9 mM MgCl2, 90 mM HEPES, 18% PEG 6000 (w/v), 1% Glycerol (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→35 Å / Num. obs: 117495 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3
Reflection shellResolution: 1.58→1.58 Å / Num. unique obs: 1207 / CC1/2: 0.886

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→25.001 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.644 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.219 5792 4.963 %
Rwork0.1986 110905 -
all0.2 --
obs-116697 99.839 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.624 Å2
Baniso -1Baniso -2Baniso -3
1--0.098 Å2-0 Å2-1.329 Å2
2--0.84 Å20 Å2
3----0.715 Å2
Refinement stepCycle: LAST / Resolution: 1.58→25.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5641 0 12 364 6017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125812
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165300
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.7967939
X-RAY DIFFRACTIONr_angle_other_deg0.3851.73612277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7595744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.51515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.13910911
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.93110236
X-RAY DIFFRACTIONr_chiral_restr0.0530.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021271
X-RAY DIFFRACTIONr_nbd_refined0.1880.2827
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.24564
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22856
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2250
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0710.210
X-RAY DIFFRACTIONr_nbd_other0.1470.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1210.216
X-RAY DIFFRACTIONr_mcbond_it1.0232.1192973
X-RAY DIFFRACTIONr_mcbond_other1.0232.1192973
X-RAY DIFFRACTIONr_mcangle_it1.7243.8053718
X-RAY DIFFRACTIONr_mcangle_other1.7243.8063719
X-RAY DIFFRACTIONr_scbond_it1.3722.2382839
X-RAY DIFFRACTIONr_scbond_other1.3732.2362838
X-RAY DIFFRACTIONr_scangle_it2.2494.0354221
X-RAY DIFFRACTIONr_scangle_other2.2494.0364222
X-RAY DIFFRACTIONr_lrange_it3.57120.9846069
X-RAY DIFFRACTIONr_lrange_other3.47520.576021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.6210.2924080.2858153X-RAY DIFFRACTION99.965
1.621-1.6650.2814700.2627904X-RAY DIFFRACTION100
1.665-1.7130.2493840.2377721X-RAY DIFFRACTION99.963
1.713-1.7660.234520.2217413X-RAY DIFFRACTION99.9619
1.766-1.8230.2273960.2087272X-RAY DIFFRACTION99.9739
1.823-1.8870.2343690.2077052X-RAY DIFFRACTION99.9731
1.887-1.9580.2493180.216831X-RAY DIFFRACTION99.7767
1.958-2.0370.2263250.2066577X-RAY DIFFRACTION99.971
2.037-2.1270.2213760.2056199X-RAY DIFFRACTION99.6967
2.127-2.230.2253230.2055986X-RAY DIFFRACTION100
2.23-2.350.2182630.2045766X-RAY DIFFRACTION99.7683
2.35-2.4910.2392640.2025418X-RAY DIFFRACTION99.9297
2.491-2.6610.2232560.1995120X-RAY DIFFRACTION99.7958
2.661-2.8710.212220.1974801X-RAY DIFFRACTION99.9602
2.871-3.1410.2322270.2024367X-RAY DIFFRACTION99.7828
3.141-3.5050.2151840.1913979X-RAY DIFFRACTION99.3793
3.505-4.0340.2032200.1773495X-RAY DIFFRACTION99.4379
4.034-4.9090.1761420.1543019X-RAY DIFFRACTION99.9684
4.909-6.8120.1851210.1852372X-RAY DIFFRACTION99.6005
6.812-100.201710.191432X-RAY DIFFRACTION99.9335

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