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- PDB-10ps: Crystal structure of SdrD A2-A3-B1-B2 domains from Staphylococcus... -

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Basic information

Entry
Database: PDB / ID: 10ps
TitleCrystal structure of SdrD A2-A3-B1-B2 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
ACETATE ION / Serine-aspartate repeat-containing protein D
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus JH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTan, K. / Gade, P. / Endres, M. / Joachimiak, 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-B1-B2 domains from Staphylococcus aureus JH1
Authors: Tan, K. / Gade, P. / Endres, M. / Joachimiak, A.
History
DepositionJan 31, 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)62,09022
Polymers61,0371
Non-polymers1,05321
Water4,612256
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)59.190, 58.570, 94.400
Angle α, β, γ (deg.)90.000, 101.350, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine-aspartate repeat-containing protein D


Mass: 61037.395 Da / Num. of mol.: 1 / Fragment: A2-A3-B1-B2 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus JH1 (bacteria)
Gene: sdrD, SAV0562 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99W47

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Non-polymers , 6 types, 277 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Tris-HCl and 20% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97856 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: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→27.2 Å / Num. obs: 42903 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.55 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.076 / Χ2: 0.97 / Net I/σ(I): 8.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2157 / CC1/2: 0.645 / Rpim(I) all: 0.876 / Χ2: 0.94 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.1 Å / SU ML: 0.2861 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6109
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 1997 4.66 %
Rwork0.2084 40861 -
obs0.2096 42858 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.97 Å2
Refinement stepCycle: LAST / Resolution: 2→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4283 0 50 256 4589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164404
X-RAY DIFFRACTIONf_angle_d0.45325985
X-RAY DIFFRACTIONf_chiral_restr0.0443683
X-RAY DIFFRACTIONf_plane_restr0.0027790
X-RAY DIFFRACTIONf_dihedral_angle_d14.88521597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.34861430.31782913X-RAY DIFFRACTION99.64
2.05-2.110.33631400.30372891X-RAY DIFFRACTION99.38
2.11-2.170.30711410.28312900X-RAY DIFFRACTION99.57
2.17-2.240.2931400.27052889X-RAY DIFFRACTION99.25
2.24-2.320.29891430.26392904X-RAY DIFFRACTION99.54
2.32-2.410.261420.25712902X-RAY DIFFRACTION99.84
2.41-2.520.29491430.25462918X-RAY DIFFRACTION99.8
2.52-2.650.28851430.23862914X-RAY DIFFRACTION99.71
2.65-2.820.28881420.24522912X-RAY DIFFRACTION99.61
2.82-3.040.2841420.23172908X-RAY DIFFRACTION99.74
3.04-3.340.26341450.20412950X-RAY DIFFRACTION99.71
3.34-3.820.20021420.1822914X-RAY DIFFRACTION98.93
3.82-4.810.15651430.14772930X-RAY DIFFRACTION98.94
4.81-27.10.17431480.16153016X-RAY DIFFRACTION99.47
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)
13.24415845107-0.879057985174-1.896046060640.5331143102580.6308892083741.47768390385-0.0626012825267-0.4067197545670.007248308601690.07733797501940.118591261621-0.05897560297140.06257931316030.269849388733-0.06215032314790.204975895507-0.0207248135442-0.03808503822420.2733425227940.00767009215730.19215384198623.8901490866-6.1921622656631.8522873911
22.85410952965-0.384247398343-0.56065570181.767334782990.1993760027774.87061724154-0.01803799234150.04136526967120.0105578912502-0.0325206904824-0.01372646994880.006719336930620.001464647539770.007961423059360.03187622390030.150351333643-0.02411836421630.0005647060812050.1897982311120.01121185172170.181858925672-1.2135967656-0.9682517772737.2089149376
33.3482536453-1.08240368002-1.155030967522.354717595930.5493707891242.11530289770.02802493156040.009708938200930.1629880473870.007893314872730.0149256824126-0.162000004181-0.100081965610.0303366797161-0.04814378193210.18899977709-0.0185258703633-0.01705448345240.160932613749-0.02096930883350.24679038313137.111044874-5.96993137445-1.0641902977
43.856137230760.250107811405-1.779655697132.20805822190.5426079959664.319934834920.2040226757530.1045583445360.192927366603-0.4271340986270.0834126861874-0.0783709977934-0.185037637198-0.0970282871603-0.2462552122060.2817904155630.0370810036618-0.003855756858680.195228074210.007223226270990.26228121727680.8688093008-15.9542939452-16.1547464126
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 445 )243 - 4451 - 203
22chain 'A' and (resid 446 through 556 )446 - 556204 - 314
33chain 'A' and (resid 557 through 677 )557 - 677315 - 435
44chain 'A' and (resid 678 through 798 )678 - 798436 - 556

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