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- PDB-9p49: Treponema denticola OppA complexed with TSGDAA and ATSAAA -

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Basic information

Entry
Database: PDB / ID: 9p49
TitleTreponema denticola OppA complexed with TSGDAA and ATSAAA
Components
  • ALA-ALA-ALA-SER-THR-ALA
  • Peptide ABC transporter, peptide-binding protein OppA
  • THR-SER-GLY-ASP-ALA-ALA
KeywordsPEPTIDE BINDING PROTEIN / Oligopeptide permease / OppABCDF / OppA
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function
Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Peptide ABC transporter, peptide-binding protein OppA
Similarity search - Component
Biological speciesTreponema denticola ATCC 35405 (bacteria)
Escherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNagy, B.G. / Suits, M.D.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-05457 Canada
CitationJournal: To Be Published
Title: The structure of a Treponema denticola oligopeptide-binding protein A, and peptide compositional preference
Authors: Nagy, B.G. / Suits, M.D.L.
History
DepositionJun 16, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 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: Peptide ABC transporter, peptide-binding protein OppA
B: ALA-ALA-ALA-SER-THR-ALA
C: Peptide ABC transporter, peptide-binding protein OppA
D: THR-SER-GLY-ASP-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7185
Polymers128,6954
Non-polymers231
Water2,864159
1
A: Peptide ABC transporter, peptide-binding protein OppA
B: ALA-ALA-ALA-SER-THR-ALA


Theoretical massNumber of molelcules
Total (without water)64,3332
Polymers64,3332
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-2 kcal/mol
Surface area22950 Å2
MethodPISA
2
C: Peptide ABC transporter, peptide-binding protein OppA
D: THR-SER-GLY-ASP-ALA-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3863
Polymers64,3632
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-13 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.320, 108.300, 213.260
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 Peptide ABC transporter, peptide-binding protein OppA


Mass: 63842.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola ATCC 35405 (bacteria)
Gene: oppA, TDE_1071 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73NT1
#2: Protein/peptide ALA-ALA-ALA-SER-THR-ALA


Mass: 490.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria)
#3: Protein/peptide THR-SER-GLY-ASP-ALA-ALA


Mass: 520.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21(DE3) (bacteria)
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.26 Å3/Da / Density % sol: 45.52 % / Description: Tetragonal Prisms, clustered
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M Na2HPO4:citirc acid, pH 4.2, 0.2 M NaCl, 22% (w/v) PEG3350, 15% (w/v) GOL, 0.05 M L-Lys, 20 mg/mL TdOppA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→48.33 Å / Num. obs: 159387 / % possible obs: 99.93 % / Redundancy: 2 % / Biso Wilson estimate: 43.08 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.05334 / Rpim(I) all: 0.05334 / Rrim(I) all: 0.07543 / Net I/σ(I): 6.78
Reflection shellResolution: 2→2.072 Å / Redundancy: 2 % / Rmerge(I) obs: 0.7828 / Num. unique obs: 7838 / CC1/2: 0.133 / CC star: 0.484 / Rpim(I) all: 0.7828 / % possible all: 99.97

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Processing

Software
NameVersionClassification
MxDCdata collection
autoPROCdata reduction
SCALAdata scaling
REFMACphasing
PHENIXmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.33 Å / SU B: 9.679 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26756 3997 5 %RANDOM
Rwork0.23809 ---
obs0.23959 79804 99.93 %-
Displacement parametersBiso mean: 58.846 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--1.06 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9106 0 1 159 9266

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