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- PDB-10pa: Crystal structure of SdrD A2-A3 domains from Staphylococcus aureus JH1 -

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Basic information

Entry
Database: PDB / ID: 10pa
TitleCrystal structure of SdrD A2-A3 domains from Staphylococcus aureus JH1
ComponentsSerine-aspartate repeat-containing protein D
KeywordsCELL ADHESION / SdrD / MSCRAMM / LPXTG-motif / Structural Genomics / PSI-Biology / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


SD-repeat containing protein, B domain / SdrD B-like domain / : / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / YSIRK type signal peptide ...SD-repeat containing protein, B domain / SdrD B-like domain / : / Fibrinogen-binding domain 2 / C-terminus of bacterial fibrinogen-binding adhesin / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Serine-aspartate repeat-containing protein D
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus JH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsTan, K. / Gade, P.R. / Endres, M. / Jochimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of SdrD A2-A3 domains from Staphylococcus aureus JH1
Authors: Tan, K. / Gade, P.R. / Endres, M. / Jochimiak, A.
History
DepositionJan 30, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine-aspartate repeat-containing protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,81710
Polymers35,3951
Non-polymers4229
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.523, 73.148, 198.705
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#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: Protein Serine-aspartate repeat-containing protein D


Mass: 35394.887 Da / Num. of mol.: 1 / Fragment: A2-A3 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus JH1 (bacteria)
Strain: JH1 / Gene: sdrD, SAV0562 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99W47
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.62 Å3/Da / Density % sol: 66.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 0.2 M calcium chloride and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.92→36.6 Å / Num. obs: 39344 / % possible obs: 98.8 % / Redundancy: 5 % / Biso Wilson estimate: 36.87 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.029 / Rrim(I) all: 0.065 / Χ2: 1.101 / Net I/σ(I): 29.2
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1851 / CC1/2: 0.539 / CC star: 0.837 / Rpim(I) all: 0.501 / Rrim(I) all: 0.99 / Χ2: 0.595 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→36.57 Å / SU ML: 0.2723 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.0568
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2449 2070 5.27 %
Rwork0.2121 37232 -
obs0.2139 39302 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.51 Å2
Refinement stepCycle: LAST / Resolution: 1.92→36.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 18 98 2574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712511
X-RAY DIFFRACTIONf_angle_d0.83753419
X-RAY DIFFRACTIONf_chiral_restr0.057402
X-RAY DIFFRACTIONf_plane_restr0.0054444
X-RAY DIFFRACTIONf_dihedral_angle_d19.1476907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.960.46641210.37272178X-RAY DIFFRACTION87.55
1.96-2.010.41221340.33912379X-RAY DIFFRACTION96.51
2.01-2.060.33861400.29752435X-RAY DIFFRACTION97.57
2.06-2.120.30591410.28142450X-RAY DIFFRACTION98.7
2.12-2.190.30241400.27242507X-RAY DIFFRACTION99.85
2.19-2.270.32961330.26022528X-RAY DIFFRACTION99.92
2.27-2.360.26731380.25492484X-RAY DIFFRACTION100
2.36-2.470.27711450.23542492X-RAY DIFFRACTION100
2.47-2.60.28191380.24462523X-RAY DIFFRACTION99.92
2.6-2.760.25751160.24462528X-RAY DIFFRACTION99.89
2.76-2.980.30391330.26512533X-RAY DIFFRACTION99.89
2.98-3.270.26341550.23492506X-RAY DIFFRACTION99.63
3.28-3.750.25021410.20482501X-RAY DIFFRACTION97.6
3.75-4.720.21691390.15952535X-RAY DIFFRACTION98.71
4.72-36.570.1651560.16082653X-RAY DIFFRACTION98.29
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.602003204940.357629034445-1.944366874114.42857827616-0.9481850573314.59466547999-0.1046847845140.540695072668-0.137990369193-0.2300592296170.06944421904750.5210091409660.150351137987-0.7772633723280.03339053389850.3913140011140.032536934768-0.1084205816950.551440485937-0.02674338898510.36216329888117.066810381211.327358233120.5467432561
22.203385618090.307434412741-1.770305671764.15119239965-1.408028607314.01378375541-0.03137351769870.312759295353-0.142049620013-0.221924871597-0.03909551436130.359206299065-0.0353940540303-0.2313659109450.0397937563570.2723360178010.0473506935977-0.03797853806540.342227622991-0.04049916017180.28139376238122.504583190410.929553239525.4988754565
32.26350865276-1.60213607961-0.8693041331313.34542543007-0.2297991739912.510392291-0.301778781495-0.207338199533-0.07053317294311.536470632770.3287581538960.596094782420.149831659399-0.1762319006260.1471991408940.8654826124220.06106503668680.3628512602360.3413165040540.05274810097620.49984332700821.7085131734-4.3864212732251.2459118034
42.8397625641-0.803394360051-0.7839504026452.58513424235-1.076282568792.39362596945-0.398597871650.208111051334-0.3300829367471.145492133690.274830763390.7821604107820.342040557683-0.2187807723750.2637722649960.683458354524-0.007339274976320.3736454921590.3091229123110.01283443161080.61210349706320.1564291343-8.8999522615245.8072719882
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 243 through 283 )243 - 2831 - 41
22chain 'A' and (resid 284 through 413 )284 - 41342 - 171
33chain 'A' and (resid 414 through 511 )414 - 511172 - 269
44chain 'A' and (resid 512 through 559 )512 - 559270 - 317

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