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- PDB-9bh3: Structure of apo Aggregatibacter actinomycetemcomitans SiaP protein -

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Basic information

Entry
Database: PDB / ID: 9bh3
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 / ACETATE ION / DctP family TRAP transporter solute-binding subunit
Function and homology information
Biological speciesAggregatibacter actinomycetemcomitans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 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 19, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,4816
Polymers136,3634
Non-polymers1182
Water88349
1
A: DctP family TRAP transporter solute-binding subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1502
Polymers34,0911
Non-polymers591
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)34,1502
Polymers34,0911
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DctP family TRAP transporter solute-binding subunit


Theoretical massNumber of molelcules
Total (without water)34,0911
Polymers34,0911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DctP family TRAP transporter solute-binding subunit


Theoretical massNumber of molelcules
Total (without water)34,0911
Polymers34,0911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.667, 141.394, 109.405
Angle α, β, γ (deg.)90.000, 112.491, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 34090.652 Da / Num. of mol.: 4
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.63 Å3/Da / Density % sol: 66.15 %
Crystal growTemperature: 292 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. Apo AaSiaP crystals that grew in SG1 conditions C11 (0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate, pH 6.5, 30% (w/v) PEG 8000)

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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: 2.58→48.64 Å / Num. obs: 61226 / % possible obs: 100 % / Redundancy: 3.6 % / CC1/2: 0.995 / Net I/σ(I): 6.3
Reflection shellResolution: 2.58→2.65 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2476 / CC1/2: 0.783

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→48.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 28.125 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21965 3158 5.2 %RANDOM
Rwork0.18906 ---
obs0.19069 58058 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.518 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å2-0.9 Å2
2--1.09 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.58→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9608 0 8 49 9665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0179798
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169388
X-RAY DIFFRACTIONr_angle_refined_deg1.531.83113238
X-RAY DIFFRACTIONr_angle_other_deg0.5221.56721676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0935.0811240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.228101748
X-RAY DIFFRACTIONr_chiral_restr0.0720.21476
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022156
X-RAY DIFFRACTIONr_mcbond_it3.4973.144894
X-RAY DIFFRACTIONr_mcbond_other3.4843.1394892
X-RAY DIFFRACTIONr_mcangle_it5.2335.6346108
X-RAY DIFFRACTIONr_mcangle_other5.2385.6356109
X-RAY DIFFRACTIONr_scbond_it4.6863.5944904
X-RAY DIFFRACTIONr_scbond_other4.6563.5914900
X-RAY DIFFRACTIONr_scangle_other7.2296.3787125
X-RAY DIFFRACTIONr_long_range_B_refined8.71431.0610747
X-RAY DIFFRACTIONr_long_range_B_other8.71431.0610744
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 243 -
Rwork0.333 4220 -
obs--99.93 %
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)
11.4790.20470.51740.9232-0.07621.95830.1257-0.09930.05940.0194-0.07-0.0814-0.05810.1312-0.05570.5816-0.01440.19470.0351-0.00630.0764-19.348-26.67729.113
21.6263-0.3767-1.02012.06710.34491.88150.0456-0.0362-0.02190.2701-0.1413-0.00470.0607-0.11190.09560.51860.0240.1250.06930.02660.0477-50.885-7.61929.864
30.82350.08170.46111.10310.56112.3069-0.10910.0996-0.0489-0.0660.13460.0094-0.02870.1367-0.02560.5013-0.0820.1590.0845-0.01630.0533-26.481-72.83826.62
42.24450.0541-0.44711.44640.44972.48710.00670.1088-0.0758-0.2121-0.03080.09750.0627-0.15230.0240.55370.10090.13660.07250.02830.0551-25.544-32.571-26.758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:308 )A3 - 308
2X-RAY DIFFRACTION2( CHAIN B AND RESID 3:308 )B3 - 308
3X-RAY DIFFRACTION3( CHAIN C AND RESID 3:308 )C3 - 308
4X-RAY DIFFRACTION4( CHAIN D AND RESID 3:308 )D3 - 308

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