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- PDB-9pv8: X-ray crystal structure of the oligopeptide-binding protein OppA3... -

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Basic information

Entry
Database: PDB / ID: 9pv8
TitleX-ray crystal structure of the oligopeptide-binding protein OppA3 from Borrelia burgdorferi
ComponentsOligopeptide-binding protein OppA3
KeywordsPEPTIDE BINDING PROTEIN / Lyme disease / spirochete / oligopeptide-binding protein
Function / homologyACETATE ION / 2-ETHOXYETHANOL / FORMIC ACID
Function and homology information
Biological speciesBorreliella burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDasteh Goli, K. / Kataria, A. / Gittis, A.G. / Garboczi, D.N. / Groshong, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: X-ray crystal structure of the oligopeptide-binding protein OppA3 from Borrelia burgdorferi
Authors: Dasteh Goli, K. / Kataria, A. / Gittis, A.G. / Garboczi, D.N. / Groshong, A.M.
History
DepositionAug 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 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: Oligopeptide-binding protein OppA3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,99241
Polymers61,6761
Non-polymers2,31640
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.550, 112.470, 139.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Oligopeptide-binding protein OppA3


Mass: 61676.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi (Lyme disease spirochete)
Production host: Escherichia coli (E. coli)

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Non-polymers , 7 types, 463 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#6: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Condition 18 from PEG/Ion 2 screen (Hampton Research, HR2-098). For cryo-protection, Condition 18 was supplement with 25% ethylene glycol
PH range: 7.0 - 8.0

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178 Å
DetectorType: DECTRIS EIGER2 R 4M / Detector: PIXEL / Date: Sep 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→29.33 Å / Num. obs: 45808 / % possible obs: 98.8 % / Redundancy: 11.627 % / Biso Wilson estimate: 20.29 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.096 / Net I/σ(I): 18.94
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 4.21 / Num. unique obs: 2938 / CC1/2: 0.888 / Rrim(I) all: 0.431

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.33 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2149 2000 4.37 %
Rwork0.1752 43743 -
obs0.177 45743 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.36 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 148 423 4605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00794284
X-RAY DIFFRACTIONf_angle_d0.90465755
X-RAY DIFFRACTIONf_chiral_restr0.0553633
X-RAY DIFFRACTIONf_plane_restr0.007730
X-RAY DIFFRACTIONf_dihedral_angle_d12.75371574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.2341240.18692713X-RAY DIFFRACTION87.43
2-2.050.22851370.17913010X-RAY DIFFRACTION96.8
2.05-2.110.24651420.1783092X-RAY DIFFRACTION99.72
2.11-2.180.23091440.17733131X-RAY DIFFRACTION100
2.18-2.260.26361420.17743120X-RAY DIFFRACTION100
2.26-2.350.22411420.17953124X-RAY DIFFRACTION100
2.35-2.460.21661440.18123143X-RAY DIFFRACTION100
2.46-2.590.24891440.17763134X-RAY DIFFRACTION100
2.59-2.750.21011420.17933125X-RAY DIFFRACTION99.97
2.75-2.960.22551460.18233166X-RAY DIFFRACTION99.97
2.96-3.260.22691450.1833179X-RAY DIFFRACTION100
3.26-3.730.20431460.17713195X-RAY DIFFRACTION100
3.73-4.690.18381480.15383225X-RAY DIFFRACTION99.91
4.69-29.330.19131540.17593386X-RAY DIFFRACTION99.44

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