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- PDB-8cqn: Crystal structure of Borrelia burgdorferi paralogous family 12 ou... -

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Basic information

Entry
Database: PDB / ID: 8cqn
TitleCrystal structure of Borrelia burgdorferi paralogous family 12 outer surface protein BBK01
ComponentsLipoprotein, putative
KeywordsDNA BINDING PROTEIN / paralogous protein / PFam12
Function / homologyProkaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein, putative
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsBrangulis, K. / Drunka, L. / Matisone, S. / Akopjana, I. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Other governmentlzp-2021/1-0068 Latvia
CitationJournal: Plos One / Year: 2024
Title: Members of the paralogous gene family 12 from the Lyme disease agent Borrelia burgdorferi are non-specific DNA-binding proteins.
Authors: Brangulis, K. / Akopjana, I. / Drunka, L. / Matisone, S. / Zelencova-Gopejenko, D. / Bhattacharya, S. / Bogans, J. / Tars, K.
History
DepositionMar 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein, putative
B: Lipoprotein, putative


Theoretical massNumber of molelcules
Total (without water)63,2922
Polymers63,2922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint-76 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.072, 52.133, 95.018
Angle α, β, γ (deg.)90.000, 90.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lipoprotein, putative


Mass: 31645.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first 4 residues (GAMG) are remnants from the expression tag.
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_K01 / Plasmid: pETm-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50805
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: 1.94 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M Bicine pH 9.0 6% PEG 20 000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2022
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.7→46.14 Å / Num. obs: 13352 / % possible obs: 98.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.3
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4 / Num. unique obs: 1771 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→46.14 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.546 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 749 5.6 %RANDOM
Rwork0.2122 ---
obs0.2139 12602 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 225.37 Å2 / Biso mean: 59.479 Å2 / Biso min: 23.07 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å2-0 Å213.58 Å2
2--55.68 Å20 Å2
3----53.1 Å2
Refinement stepCycle: final / Resolution: 2.7→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3004 0 0 0 3004
Num. residues----372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133027
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173006
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.6384047
X-RAY DIFFRACTIONr_angle_other_deg1.4151.5877017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7555370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32523.963164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.5915664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5281520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023274
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02546
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 53 -
Rwork0.257 944 -
all-997 -
obs--98.23 %

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