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- PDB-6shu: Borrelia burgdorferi BmpD nucleoside binding protein bound to ade... -

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Basic information

Entry
Database: PDB / ID: 6shu
TitleBorrelia burgdorferi BmpD nucleoside binding protein bound to adenosine
ComponentsBasic membrane protein D
KeywordsTRANSPORT PROTEIN / transporter / nucleoside / purine
Function / homologyABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / ADENOSINE / Basic membrane protein D
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43002869382 Å
AuthorsGuedez, G. / Astrand, M. / Cuellar, J. / Hytonen, J. / Salminen, T.A.
Funding support Finland, 1items
OrganizationGrant numberCountry
Sigrid Juselius Foundation Finland
CitationJournal: Infect.Immun. / Year: 2020
Title: Structural and Biomolecular Analyses of Borrelia burgdorferi BmpD Reveal a Substrate-Binding Protein of an ABC-Type Nucleoside Transporter Family.
Authors: Cuellar, J. / Astrand, M. / Elovaara, H. / Pietikainen, A. / Siren, S. / Liljeblad, A. / Guedez, G. / Salminen, T.A. / Hytonen, J.
History
DepositionAug 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Basic membrane protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6184
Polymers39,2921
Non-polymers3263
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, protein ligand binding assays
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-9 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.780, 42.900, 66.380
Angle α, β, γ (deg.)90.000, 117.339, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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Components

#1: Protein Basic membrane protein D


Mass: 39292.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (strain JD1) (bacteria)
Strain: JD1 / Gene: bmpD, BbuJD1_0385 / Production host: Escherichia coli (E. coli) / References: UniProt: E4S1L1
#2: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#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 / Water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M CaCl2, 0.1 M NaAcetate pH 5.0, 20 % PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.43→58.97 Å / Num. obs: 44945 / % possible obs: 92 % / Redundancy: 7.6 % / Biso Wilson estimate: 11.4009465962 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06223 / Rrim(I) all: 0.06662 / Net I/σ(I): 19.34
Reflection shellResolution: 1.43→1.481 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.3157 / Mean I/σ(I) obs: 3.86 / Num. unique obs: 2652 / CC1/2: 0.915 / Rrim(I) all: 0.3546 / % possible all: 51.3

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIX1.10.1_2155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43002869382→30.7054995969 Å / SU ML: 0.109588610386 / Cross valid method: THROUGHOUT / σ(F): 1.36089495234 / Phase error: 18.8856208632
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.179340033578 2193 4.87929691846 %RANDOM
Rwork0.153557668964 42752 --
obs0.154848832023 44945 90.6441594063 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.2831965041 Å2
Refinement stepCycle: LAST / Resolution: 1.43002869382→30.7054995969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 21 409 2846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005223453060032523
X-RAY DIFFRACTIONf_angle_d0.8061530551533409
X-RAY DIFFRACTIONf_chiral_restr0.0811537619126380
X-RAY DIFFRACTIONf_plane_restr0.00429442412469439
X-RAY DIFFRACTIONf_dihedral_angle_d15.1219082681918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43002869382-1.48110.2163800.18562498X-RAY DIFFRACTION51.3170731707
3.6016-30.70549959690.1422414326681370.1356295927673067X-RAY DIFFRACTION99.8753117207
Refinement TLS params.Method: refined / Origin x: 9.47545137734 Å / Origin y: 21.9707822093 Å / Origin z: 16.2846815386 Å
111213212223313233
T0.0487676386732 Å2-1.07406789163E-5 Å20.00236973446401 Å2-0.0218004793321 Å20.000447308993928 Å2--0.0393462720394 Å2
L0.750511259047 °2-0.0170712475259 °20.15621700868 °2-0.158064622969 °2-0.00320155112857 °2--0.611648767873 °2
S-0.00479527228019 Å °-0.0286507794374 Å °-0.0231623093224 Å °-0.0139585112101 Å °0.00701545071918 Å °-0.00489442298294 Å °0.00131290631122 Å °-0.0440485800639 Å °0.000473574288715 Å °
Refinement TLS groupSelection details: all

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