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- PDB-9q1u: Borrelia burgdorferi BmpA bound to thymidine -

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Basic information

Entry
Database: PDB / ID: 9q1u
TitleBorrelia burgdorferi BmpA bound to thymidine
ComponentsBasic membrane protein A
KeywordsTRANSPORT PROTEIN / Substrate binding protein / nucleoside binding protein
Function / homology: / ABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Periplasmic binding protein-like I / membrane / plasma membrane / ACETATE ION / THYMIDINE / Basic membrane protein A
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsLiu, Q. / Fernandez, D. / Sharaf, N.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Structural basis for selective thymidine binding by the Borrelia burgdorferi substrate-binding protein BmpA.
Authors: Liu, Q. / Nun Ez, V.A. / Fernandez, D. / Stewart, C.J. / Sharaf, N.G.
History
DepositionAug 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Basic membrane protein A
B: Basic membrane protein A
C: Basic membrane protein A
D: Basic membrane protein A
E: Basic membrane protein A
F: Basic membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,22116
Polymers215,5426
Non-polymers1,67910
Water1,11762
1
A: Basic membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2623
Polymers35,9241
Non-polymers3382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Basic membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2013
Polymers35,9241
Non-polymers2782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Basic membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1662
Polymers35,9241
Non-polymers2421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Basic membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2013
Polymers35,9241
Non-polymers2782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Basic membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1662
Polymers35,9241
Non-polymers2421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Basic membrane protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2253
Polymers35,9241
Non-polymers3012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.274, 133.172, 191.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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, 6 molecules ABCDEF

#1: Protein
Basic membrane protein A / Immunodominant antigen P39 / Probable substrate-binding protein BmpA


Mass: 35923.652 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: bmpA, BB_0383 / Production host: Escherichia coli (E. coli) / References: UniProt: Q45010

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Non-polymers , 5 types, 72 molecules

#2: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium chloride, 0.1 M Sodium acetate, 0.1 M Lithium sulfate, 12% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.58→51.42 Å / Num. obs: 80623 / % possible obs: 95 % / Redundancy: 3.5 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.174 / Net I/σ(I): 4.5
Reflection shellResolution: 2.58→2.74 Å / Num. unique obs: 11985 / CC1/2: 0.156

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→50.6 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3081 4014 5.1 %
Rwork0.254 --
obs0.2567 78683 91.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.58→50.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14490 0 113 62 14665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314857
X-RAY DIFFRACTIONf_angle_d0.57320031
X-RAY DIFFRACTIONf_dihedral_angle_d4.4261998
X-RAY DIFFRACTIONf_chiral_restr0.0432238
X-RAY DIFFRACTIONf_plane_restr0.0032563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.610.50481090.54291825X-RAY DIFFRACTION66
2.61-2.640.53591140.50962209X-RAY DIFFRACTION80
2.64-2.680.47641340.47452415X-RAY DIFFRACTION87
2.68-2.710.53581180.46182507X-RAY DIFFRACTION89
2.71-2.750.47471260.44232562X-RAY DIFFRACTION92
2.75-2.790.41261600.4262635X-RAY DIFFRACTION95
2.79-2.830.50121380.41222631X-RAY DIFFRACTION95
2.83-2.870.45581530.40772632X-RAY DIFFRACTION94
2.87-2.920.45551360.38172676X-RAY DIFFRACTION96
2.92-2.970.41321330.38182663X-RAY DIFFRACTION95
2.97-3.030.41631390.36672675X-RAY DIFFRACTION96
3.03-3.080.40211360.35792685X-RAY DIFFRACTION96
3.08-3.150.40561410.3452663X-RAY DIFFRACTION95
3.15-3.220.37351460.35082660X-RAY DIFFRACTION95
3.22-3.290.42561410.31232638X-RAY DIFFRACTION95
3.29-3.370.36291210.30322637X-RAY DIFFRACTION94
3.37-3.460.36341590.29752626X-RAY DIFFRACTION94
3.46-3.570.3511340.28112604X-RAY DIFFRACTION93
3.57-3.680.35451450.26082507X-RAY DIFFRACTION90
3.68-3.810.3011460.25072628X-RAY DIFFRACTION94
3.81-3.960.30261590.2412631X-RAY DIFFRACTION94
3.96-4.140.31490.21232641X-RAY DIFFRACTION94
4.14-4.360.28221610.19362609X-RAY DIFFRACTION93
4.36-4.640.26181270.19272618X-RAY DIFFRACTION92
4.64-4.990.22851340.19312641X-RAY DIFFRACTION93
4.99-5.50.21261200.18672649X-RAY DIFFRACTION92
5.5-6.290.3191570.2222586X-RAY DIFFRACTION91
6.29-7.920.23151520.19512520X-RAY DIFFRACTION88
7.92-50.60.19371260.17832696X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: -41.6231 Å / Origin y: -3.7573 Å / Origin z: -37.5809 Å
111213212223313233
T0.7194 Å2-0.0152 Å2-0.0783 Å2-0.4221 Å20.0579 Å2--0.5296 Å2
L0.3871 °2-0.0234 °2-0.1292 °2-0.3234 °20.2335 °2--0.6012 °2
S-0.0139 Å °-0.0559 Å °0.0178 Å °0.0593 Å °-0.0217 Å °0.0416 Å °0.0375 Å °0.0348 Å °0.039 Å °
Refinement TLS groupSelection details: all

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