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- PDB-9ru4: Crystal structure of a sialic acid binding protein, Q216A mutant,... -

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Basic information

Entry
Database: PDB / ID: 9ru4
TitleCrystal structure of a sialic acid binding protein, Q216A 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: 1.6 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 3, 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)97,3206
Polymers96,5102
Non-polymers8114
Water20,3571130
1
A: Sugar ABC transporter, sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6603
Polymers48,2551
Non-polymers4052
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)48,6603
Polymers48,2551
Non-polymers4052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.831, 61.493, 89.394
Angle α, β, γ (deg.)90.000, 106.230, 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: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 40 - 436 / Label seq-ID: 37 - 433

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: 48254.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: mutant Q216A
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.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1130 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
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: 1.6→66.78 Å / Num. obs: 106140 / % possible obs: 97.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 10.64 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.107 / Net I/σ(I): 12.9 / Num. measured all: 751307
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.6-1.637.12.23635250930.1880.50993.7
4.34-66.846.740.13753155760.020.0599.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALSdata reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→66.778 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.8 / SU ML: 0.075 / Cross valid method: FREE R-VALUE / ESU R: 0.135 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2308 1989 1.875 %
Rwork0.1803 104096 -
all0.181 --
obs-106085 97.671 %
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: 12.969 Å2
Baniso -1Baniso -2Baniso -3
1-2.542 Å20 Å20.396 Å2
2---0.719 Å2-0 Å2
3----1.756 Å2
Refinement stepCycle: LAST / Resolution: 1.6→66.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6229 0 52 1130 7411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126626
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166164
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.8169011
X-RAY DIFFRACTIONr_angle_other_deg0.5731.77814341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8125849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.021512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89101148
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.90410302
X-RAY DIFFRACTIONr_chiral_restr0.0830.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027791
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021457
X-RAY DIFFRACTIONr_nbd_refined0.2240.21391
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.25547
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23366
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.23178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2742
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.218
X-RAY DIFFRACTIONr_nbd_other0.2260.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1680.22
X-RAY DIFFRACTIONr_mcbond_it2.7361.3093279
X-RAY DIFFRACTIONr_mcbond_other2.7281.3093279
X-RAY DIFFRACTIONr_mcangle_it4.0292.3554125
X-RAY DIFFRACTIONr_mcangle_other4.032.3564126
X-RAY DIFFRACTIONr_scbond_it3.7991.4763347
X-RAY DIFFRACTIONr_scbond_other3.7671.4713338
X-RAY DIFFRACTIONr_scangle_it5.6512.6254872
X-RAY DIFFRACTIONr_scangle_other5.6142.6154861
X-RAY DIFFRACTIONr_lrange_it10.91317.218158
X-RAY DIFFRACTIONr_lrange_other9.58513.8697802
X-RAY DIFFRACTIONr_rigid_bond_restr2.969312790
X-RAY DIFFRACTIONr_ncsr_local_group_10.0580.0513666
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.05850.0501
12BX-RAY DIFFRACTIONLocal ncs0.05850.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6410.2611520.2227474X-RAY DIFFRACTION94.8036
1.641-1.6860.2871180.1997342X-RAY DIFFRACTION96.3326
1.686-1.7350.2181320.1857143X-RAY DIFFRACTION96.5879
1.735-1.7880.2461300.1627058X-RAY DIFFRACTION96.8994
1.788-1.8470.2191360.166770X-RAY DIFFRACTION97.0353
1.847-1.9110.2221150.156588X-RAY DIFFRACTION97.1872
1.911-1.9830.2121290.1486377X-RAY DIFFRACTION97.3806
1.983-2.0640.2171290.1436146X-RAY DIFFRACTION98.0775
2.064-2.1560.2331110.1485916X-RAY DIFFRACTION98.0478
2.156-2.2610.197930.1465683X-RAY DIFFRACTION97.8817
2.261-2.3830.1981070.1465410X-RAY DIFFRACTION98.2197
2.383-2.5280.19960.165150X-RAY DIFFRACTION98.8878
2.528-2.7020.25980.1674820X-RAY DIFFRACTION98.36
2.702-2.9180.222910.1754541X-RAY DIFFRACTION99.0167
2.918-3.1960.234780.1924162X-RAY DIFFRACTION99.2277
3.196-3.5720.227800.1983789X-RAY DIFFRACTION99.2051
3.572-4.1230.249710.1863334X-RAY DIFFRACTION99.3291
4.123-5.0450.216610.2092862X-RAY DIFFRACTION99.7271
5.045-7.1140.309430.292240X-RAY DIFFRACTION99.7815
7.114-66.7780.372190.3351291X-RAY DIFFRACTION99.6956

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