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- PDB-8p32: BB0238 from Borrelia burgdorferi, Se-Met data for Leu240Met mutant -

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Open data


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Basic information

Entry
Database: PDB / ID: 8p32
TitleBB0238 from Borrelia burgdorferi, Se-Met data for Leu240Met mutant
ComponentsBB0238
KeywordsMEMBRANE PROTEIN / Lyme disease / borreliosis / outer surface protein / immune evasion
Function / homologymembrane / Uncharacterized protein
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsBrangulis, K. / Foor, S.D. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Linden, S.B. / Altieri, A.S. / Akopjana, I. ...Brangulis, K. / Foor, S.D. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Linden, S.B. / Altieri, A.S. / Akopjana, I. / Baljinnyam, B. / Nelson, D.C. / Simeonov, A. / Herzberg, O. / Caimano, M.J. / Pal, U.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Other governmentlzp-2020/2-0378 Latvia
CitationJournal: Mbio / Year: 2023
Title: A unique borrelial protein facilitates microbial immune evasion.
Authors: Foor, S.D. / Brangulis, K. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Alreja, A.B. / Linden, S.B. / Altieri, A.S. / Baljinnyam, B. / Akopjana, I. / Nelson, D.C. / ...Authors: Foor, S.D. / Brangulis, K. / Shakya, A.K. / Rana, V.S. / Bista, S. / Kitsou, C. / Ronzetti, M. / Alreja, A.B. / Linden, S.B. / Altieri, A.S. / Baljinnyam, B. / Akopjana, I. / Nelson, D.C. / Simeonov, A. / Herzberg, O. / Caimano, M.J. / Pal, U.
History
DepositionMay 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: BB0238


Theoretical massNumber of molelcules
Total (without water)16,3861
Polymers16,3861
Non-polymers00
Water82946
1
D: BB0238

D: BB0238


Theoretical massNumber of molelcules
Total (without water)32,7732
Polymers32,7732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area1700 Å2
ΔGint-12 kcal/mol
Surface area12110 Å2
Unit cell
Length a, b, c (Å)55.259, 55.259, 94.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein BB0238


Mass: 16386.291 Da / Num. of mol.: 1 / Mutation: Leu240Met
Source method: isolated from a genetically manipulated source
Details: First 4 residues (GAMG) are remnants from the expression tag after TEV protease cleavage. There is a mutation Leu240Met introduced.
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_0238 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O51254
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2.6 M ammonium sulfate 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.15→94.53 Å / Num. obs: 8541 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 24.1
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 9.8 / Num. unique obs: 674 / CC1/2: 0.982 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→47.71 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.262 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 415 4.9 %RANDOM
Rwork0.2016 ---
obs0.2045 8051 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.63 Å2 / Biso mean: 38.948 Å2 / Biso min: 22.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 2.15→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 0 46 1061
Biso mean---44.12 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131051
X-RAY DIFFRACTIONr_bond_other_d0.0020.016971
X-RAY DIFFRACTIONr_angle_refined_deg1.611.631415
X-RAY DIFFRACTIONr_angle_other_deg1.3031.6012239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7042558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39615192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.954153
X-RAY DIFFRACTIONr_chiral_restr0.0810.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 32 -
Rwork0.183 575 -
all-607 -
obs--100 %

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