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- PDB-9bhf: Structure of apo Aggregatibacter actinomycetemcomitans SiaP protein -

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Basic information

Entry
Database: PDB / ID: 9bhf
TitleStructure of apo Aggregatibacter actinomycetemcomitans SiaP protein
ComponentsDctP family TRAP transporter solute-binding subunit
KeywordsMEMBRANE PROTEIN / SOME MACROMOLECULE
Function / homologyTRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / N-acetyl-beta-neuraminic acid / DctP family TRAP transporter solute-binding subunit
Function and homology information
Biological speciesAggregatibacter actinomycetemcomitans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKing-Hudson, T.-R.J. / Davies, J.S. / Dobson, R.C.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden FundUOC1506 New Zealand
CitationJournal: To Be Published
Title: Structure of apo Aggregatibacter actinomycetemcomitans SiaP protein
Authors: King-Hudson, T.-R.J. / Davies, J.S.
History
DepositionApr 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DctP family TRAP transporter solute-binding subunit
B: DctP family TRAP transporter solute-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2924
Polymers68,6742
Non-polymers6192
Water8,773487
1
A: DctP family TRAP transporter solute-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6462
Polymers34,3371
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DctP family TRAP transporter solute-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6462
Polymers34,3371
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.166, 49.540, 121.389
Angle α, β, γ (deg.)90.000, 92.810, 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

#1: Protein DctP family TRAP transporter solute-binding subunit / SiaP


Mass: 34336.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aggregatibacter actinomycetemcomitans (bacteria)
Gene: FXB68_07930 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5D0EK58
#2: 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 / Feature type: SUBJECT OF INVESTIGATION
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Drops consisting of 400 nL of mother-liquor and protein solution (AaSiaP at 20 mg/mL along with and without 0.75 mM Neu5Ac in SEC buffer) were mixed using the Mosquito Protein ...Details: Drops consisting of 400 nL of mother-liquor and protein solution (AaSiaP at 20 mg/mL along with and without 0.75 mM Neu5Ac in SEC buffer) were mixed using the Mosquito Protein Crystallization System and the sitting-drop vapor-diffusion method and incubated at 20 C. Neu5Ac (0.75 mM) bound AaSiaP crystals including grew in SG1 condition H2 (30% w/v PEG 4000) were not cryo-protected before being flash-cooled in liquid nitrogen prior to data collection

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→45.86 Å / Num. obs: 62386 / % possible obs: 99.76 % / Redundancy: 2 % / Biso Wilson estimate: 25.77 Å2 / CC1/2: 0.995 / Net I/σ(I): 6.2
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 6175 / CC1/2: 0.505

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→45.81 Å / SU ML: 0.2346 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.0398
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2317 3107 4.98 %
Rwork0.1999 59261 -
obs0.2015 62368 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 42 487 5347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01435005
X-RAY DIFFRACTIONf_angle_d1.41576779
X-RAY DIFFRACTIONf_chiral_restr0.0748761
X-RAY DIFFRACTIONf_plane_restr0.013879
X-RAY DIFFRACTIONf_dihedral_angle_d6.9058669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.35281270.33732668X-RAY DIFFRACTION99.89
1.93-1.960.33581280.31242686X-RAY DIFFRACTION99.93
1.96-20.32591430.28992649X-RAY DIFFRACTION99.93
2-2.030.32641450.27842668X-RAY DIFFRACTION100
2.03-2.070.31011560.26422705X-RAY DIFFRACTION99.97
2.07-2.110.28131510.24642631X-RAY DIFFRACTION99.96
2.11-2.160.30191520.2492663X-RAY DIFFRACTION100
2.16-2.210.26821110.24612716X-RAY DIFFRACTION99.89
2.21-2.260.28591410.23952673X-RAY DIFFRACTION99.96
2.26-2.330.26861150.22152677X-RAY DIFFRACTION99.96
2.33-2.390.23061120.21412715X-RAY DIFFRACTION99.89
2.39-2.470.24311480.20172700X-RAY DIFFRACTION100
2.47-2.560.24091470.19912663X-RAY DIFFRACTION100
2.56-2.660.24391550.19262693X-RAY DIFFRACTION100
2.66-2.780.22731630.20052661X-RAY DIFFRACTION99.93
2.78-2.930.23541550.20232672X-RAY DIFFRACTION99.93
2.93-3.110.27271500.2042696X-RAY DIFFRACTION99.96
3.11-3.350.24721290.20152713X-RAY DIFFRACTION100
3.35-3.690.19711630.19382691X-RAY DIFFRACTION100
3.69-4.220.18741110.16322761X-RAY DIFFRACTION100
4.23-5.320.15191630.14762715X-RAY DIFFRACTION100
5.32-45.810.21371420.16022845X-RAY DIFFRACTION99.8

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