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- PDB-9rsl: Crystal structure of a sialic acid binding protein, R113A mutant,... -

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Basic information

Entry
Database: PDB / ID: 9rsl
TitleCrystal structure of a sialic acid binding protein, R113A mutant, from Streptococcus pneumoniae bound to Neu5Ac
ComponentsSugar ABC transporter, sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / Sialic acid / Neu5Ac / Periplasmic binding protein / Streptococcus pneumoniae / mutant
Function / homologymaltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / N-acetyl-alpha-neuraminic acid / Sugar ABC transporter, sugar-binding protein
Function and homology information
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAtkinson, M. / Lukacik, P. / Strain-Damerell, C.M. / Gloster, T.M. / Walsh, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: To Be Published / Year: 2026
Title: Structure of S. pneumoniae sialic acid binding protein; SatA
Authors: Strain-Damerell, C.M. / Atkinson, M. / Meller, C. / Harris, G. / Gloster, T.M. / Lukacik, P. / Walsh, M.A.
History
DepositionJul 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 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: Sugar ABC transporter, sugar-binding protein
B: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,62111
Polymers96,4522
Non-polymers1,1709
Water23,8161322
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Elutes at appropriate point for monomeric protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-57 kcal/mol
Surface area33400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.347, 89.404, 151.269
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 40 - 438 / Label seq-ID: 37 - 435

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Sugar ABC transporter, sugar-binding protein


Mass: 48225.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Mutant R113A
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Gene: SP_1683 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: A0A0H2URD1
#2: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19NO9 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4 / Details: 0.1M NaCit, 3.6M ammonium sulfate, pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→57.74 Å / Num. obs: 92279 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 11.65 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.184 / Net I/σ(I): 8.5 / Num. measured all: 1253922
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.7-1.7313.71.46102144580.2731.01898.3
4.61-57.7812.726.86329649660.0180.066100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALSdata reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→57.74 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.873 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1982 2016 2.187 %
Rwork0.1715 90154 -
all0.172 --
obs-92170 99.935 %
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: 15.332 Å2
Baniso -1Baniso -2Baniso -3
1--1.349 Å20 Å20 Å2
2---0.931 Å20 Å2
3---2.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6253 0 69 1322 7644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126681
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166185
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.8179076
X-RAY DIFFRACTIONr_angle_other_deg0.5541.77814393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7945848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.176510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.968101156
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.48110305
X-RAY DIFFRACTIONr_chiral_restr0.0820.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027833
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021455
X-RAY DIFFRACTIONr_nbd_refined0.240.21421
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.25584
X-RAY DIFFRACTIONr_nbtor_refined0.1830.23426
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.23162
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2976
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.060.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2280.222
X-RAY DIFFRACTIONr_nbd_other0.2310.2106
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.296
X-RAY DIFFRACTIONr_mcbond_it1.2081.5093308
X-RAY DIFFRACTIONr_mcbond_other1.2061.5093308
X-RAY DIFFRACTIONr_mcangle_it1.8052.7074163
X-RAY DIFFRACTIONr_mcangle_other1.8062.7084164
X-RAY DIFFRACTIONr_scbond_it2.5981.7943373
X-RAY DIFFRACTIONr_scbond_other2.5021.773352
X-RAY DIFFRACTIONr_scangle_it4.0973.1414906
X-RAY DIFFRACTIONr_scangle_other4.0143.0984877
X-RAY DIFFRACTIONr_lrange_it5.98322.0628504
X-RAY DIFFRACTIONr_lrange_other5.57116.8737985
X-RAY DIFFRACTIONr_ncsr_local_group_10.0470.0513890
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.047270.0501
12BX-RAY DIFFRACTIONLocal ncs0.047270.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3021630.3086533X-RAY DIFFRACTION99.5392
1.744-1.7920.2861280.2896436X-RAY DIFFRACTION99.9543
1.792-1.8440.3041420.2646229X-RAY DIFFRACTION99.9843
1.844-1.90.2451250.2386106X-RAY DIFFRACTION99.984
1.9-1.9630.2251160.2095884X-RAY DIFFRACTION99.9667
1.963-2.0320.2261400.1865698X-RAY DIFFRACTION99.9829
2.032-2.1080.211150.1655526X-RAY DIFFRACTION99.9823
2.108-2.1940.191270.1565307X-RAY DIFFRACTION99.9816
2.194-2.2910.1731020.1465104X-RAY DIFFRACTION100
2.291-2.4030.1651380.1414865X-RAY DIFFRACTION100
2.403-2.5330.1851120.1454627X-RAY DIFFRACTION99.9578
2.533-2.6860.154910.154417X-RAY DIFFRACTION99.9557
2.686-2.8710.193860.1454179X-RAY DIFFRACTION99.9766
2.871-3.1010.2800.1573903X-RAY DIFFRACTION100
3.101-3.3960.218820.1543582X-RAY DIFFRACTION99.9727
3.396-3.7950.172690.1393248X-RAY DIFFRACTION100
3.795-4.3790.143710.1222902X-RAY DIFFRACTION100
4.379-5.3550.139560.142466X-RAY DIFFRACTION99.9604
5.355-7.5410.228500.1921963X-RAY DIFFRACTION100
7.541-57.740.224230.211172X-RAY DIFFRACTION100

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