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- PDB-9ht3: Crystal structure of PA0884, the SBP component of a Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 9ht3
TitleCrystal structure of PA0884, the SBP component of a Pseudomonas aeruginosa PAO1 Tripartite ATP-independent Periplasmic (TRAP) transporter, complexed with itaconate
ComponentsProbable C4-dicarboxylate-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / periplasmic substrate binding protein / C4-dicarboxylate transport / itaconate
Function / homology
Function and homology information


C4-dicarboxylate transport / transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
2-methylidenebutanedioic acid / Probable C4-dicarboxylate-binding periplasmic protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHerman, R. / Mehboob, J. / Elston, R. / Afolabi, H. / Kinniment-Williams, B.E. / Wilkinson, A.J. / Thomas, G.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Biochem.J. / Year: 2025
Title: Itaconate utilisation by the human pathogen Pseudomonas aeruginosa requires uptake via the IctPQM TRAP transporter.
Authors: Mehboob, J. / Herman, R. / Elston, R.C. / Afolabi, H. / Kinniment-Williams, B.E. / van der Woude, M.W. / Wilkinson, A.J. / Thomas, G.H.
History
DepositionDec 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable C4-dicarboxylate-binding periplasmic protein
B: Probable C4-dicarboxylate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3787
Polymers69,8712
Non-polymers5065
Water6,738374
1
A: Probable C4-dicarboxylate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2504
Polymers34,9361
Non-polymers3143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable C4-dicarboxylate-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1283
Polymers34,9361
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.206, 117.490, 166.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable C4-dicarboxylate-binding periplasmic protein


Mass: 34935.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0884 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I561
#2: Chemical ChemComp-ITN / 2-methylidenebutanedioic acid


Mass: 130.099 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: JCSG-plus HT-96 D12: 0.04 M Potassium phosphate monobasic, 16 % w/v PEG 8000, 20 % v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→50.07 Å / Num. obs: 63463 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.308 / Rpim(I) all: 0.126 / Rrim(I) all: 0.333 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-50.0711.10.05568840.9980.0220.059
1.8-1.8413.63.617497620.3541.4693.908

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→50.07 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.829 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23205 3204 5.1 %RANDOM
Rwork0.18541 ---
obs0.18783 60163 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.042 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å2-0 Å2
2--0.62 Å20 Å2
3---1.63 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4885 0 34 374 5293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0125005
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5751.8326750
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.172546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76810888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1640.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023876
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6562.2012442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3863.9383049
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1482.6512563
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.79225.337881
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 215 -
Rwork0.31 4326 -
obs--99.96 %

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