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- PDB-9ry2: Crystal structure of a sialic acid binding protein, R113K:G213Q:Q... -

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Basic information

Entry
Database: PDB / ID: 9ry2
TitleCrystal structure of a sialic acid binding protein, R113K:G213Q:Q216N mutant, from Streptococcus pneumoniae bound to Neu5Ac
ComponentsSugar ABC transporter, sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / Sialic acid / Neu5Ac / Periplasmic binding protein / Streptococcus pneumoniae
Function / homology
Function and homology information


maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
Similarity search - Function
Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
CITRIC ACID / N-acetyl-alpha-neuraminic acid / N-acetyl-beta-neuraminic acid / Sugar ABC transporter, sugar-binding protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsStrain-Damerell, C.M. / Lukacik, P. / Atkinson, 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 14, 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)98,2078
Polymers96,6822
Non-polymers1,5256
Water9,890549
1
A: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5576
Polymers48,3411
Non-polymers1,2165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6502
Polymers48,3411
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.359, 61.485, 89.296
Angle α, β, γ (deg.)90.000, 106.288, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 41 - 438 / Label seq-ID: 38 - 435

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

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

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 48341.000 Da / Num. of mol.: 2 / Mutation: R113K, G213Q, Q216N
Source method: isolated from a genetically manipulated source
Details: R113K:G213Q:Q216N mutant
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

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Sugars , 2 types, 4 molecules

#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: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 551 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Sodium citrate, pH 5 3.2 M Ammonium sulphate

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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: 2→67.033 Å / Num. obs: 55915 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 14.61 Å2 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.109 / Rrim(I) all: 0.292 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2-2.047.21.41936427080.4651.25397.2
5.43-67.07719.72039329160.0350.093100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→67.033 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.09 / SU ML: 0.159 / Cross valid method: FREE R-VALUE / ESU R: 0.212 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2443 1967 3.52 %
Rwork0.2038 53913 -
all0.205 --
obs-55880 99.821 %
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: 20.877 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.023 Å2
2--0.047 Å2-0 Å2
3---0.117 Å2
Refinement stepCycle: LAST / Resolution: 2.001→67.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6255 0 102 549 6906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126499
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166045
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.8158804
X-RAY DIFFRACTIONr_angle_other_deg0.5861.77514031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.519510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.625101108
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.13910290
X-RAY DIFFRACTIONr_chiral_restr0.0830.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027497
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021411
X-RAY DIFFRACTIONr_nbd_refined0.2140.21364
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.25484
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23346
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23252
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2503
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2920.218
X-RAY DIFFRACTIONr_nbd_other0.1610.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.233
X-RAY DIFFRACTIONr_mcbond_it1.7012.0273194
X-RAY DIFFRACTIONr_mcbond_other1.7012.0273194
X-RAY DIFFRACTIONr_mcangle_it2.4333.6393989
X-RAY DIFFRACTIONr_mcangle_other2.4333.643990
X-RAY DIFFRACTIONr_scbond_it2.842.3953305
X-RAY DIFFRACTIONr_scbond_other2.832.3923302
X-RAY DIFFRACTIONr_scangle_it4.5234.234815
X-RAY DIFFRACTIONr_scangle_other4.5224.234816
X-RAY DIFFRACTIONr_lrange_it5.58221.6057693
X-RAY DIFFRACTIONr_lrange_other5.58321.6087694
X-RAY DIFFRACTIONr_ncsr_local_group_10.0520.0513418
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.051840.0501
12BX-RAY DIFFRACTIONLocal ncs0.051840.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.001-2.0530.3041220.29139260.29241280.9320.93698.0620.269
2.053-2.110.3171580.27338280.27539910.9210.94699.87470.254
2.11-2.1710.3291190.25737720.25938940.9260.95599.9230.23
2.171-2.2370.2841320.23736660.23937990.9510.96299.97370.208
2.237-2.3110.2441400.2135250.21136670.9610.97199.94550.181
2.311-2.3920.2521240.21534250.21635500.9570.96999.97180.184
2.392-2.4820.2411370.20433010.20634380.9620.9731000.173
2.482-2.5830.2621090.20231950.20433050.9560.97499.96970.17
2.583-2.6980.2851110.21730760.21931890.9540.97199.93730.184
2.698-2.8290.2371320.20628850.20730180.960.97399.96690.173
2.829-2.9820.2481060.19227740.19428800.9560.9771000.166
2.982-3.1620.245890.20426410.20627300.9640.9751000.18
3.162-3.380.229850.19525130.19625990.9710.9899.96150.178
3.38-3.650.193770.17123040.17223810.9750.9841000.155
3.65-3.9970.218800.16521380.16722180.9740.9841000.147
3.997-4.4670.187750.15619390.15720140.9770.9861000.14
4.467-5.1550.23610.16717230.16917840.9720.9851000.147
5.155-6.3040.211410.19514720.19615140.9790.9899.9340.172
6.304-8.8760.227410.2111510.21111920.970.9761000.189
8.876-67.0330.233280.2366580.2366860.9690.9671000.232

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