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- PDB-6fxe: BBE31 from Lyme disease agent Borrelia (Borreliella) burgdorferi ... -

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Basic information

Entry
Database: PDB / ID: 6fxe
TitleBBE31 from Lyme disease agent Borrelia (Borreliella) burgdorferi playing a vital role in successful colonization of the mammalian host
ComponentsPutative surface proteinCell membrane
KeywordsPROTEIN BINDING / Outer surface protein / borrelia outer membrane / pFam54 family / glutathione binding
Function / homologyBorrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / GLUTATHIONE / Putative surface protein
Function and homology information
Biological speciesBorrelia burgdorferi B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsBrangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
ERDF/CFCA/SEDA1.1.1.2/VIAA/1/16/144 Latvia
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: BBE31 from the Lyme disease agent Borrelia burgdorferi, known to play an important role in successful colonization of the mammalian host, shows the ability to bind glutathione.
Authors: Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Zelencova, D. / Jekabsons, A. / Jaudzems, K. / Tars, K.
History
DepositionMar 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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: Putative surface protein
B: Putative surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1264
Polymers48,5122
Non-polymers6152
Water1448
1
A: Putative surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5632
Polymers24,2561
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5632
Polymers24,2561
Non-polymers3071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.390, 75.270, 87.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative surface protein / Cell membrane


Mass: 24255.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: First four amino acids (GAMG) are remnants from the expression tag.
Source: (gene. exp.) Borrelia burgdorferi B31 (bacteria) / Gene: BB_E31 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O50725
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M Ammonium sulfate 0.1M Sodium acetate 26% PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 2, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.4→75.17 Å / Num. obs: 19149 / % possible obs: 96.6 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 2777 / % possible all: 98.1

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→57.19 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.186 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.434 / ESU R Free: 0.276
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 982 5.1 %RANDOM
Rwork0.2068 ---
obs0.2094 18138 96.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.66 Å2 / Biso mean: 45.507 Å2 / Biso min: 18.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.4→57.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 40 8 3362
Biso mean--82.23 33.19 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023396
X-RAY DIFFRACTIONr_bond_other_d0.0020.023387
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.9994557
X-RAY DIFFRACTIONr_angle_other_deg0.89137847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1775404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.07526.601153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.11915711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.183158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023737
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02707
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 80 -
Rwork0.244 1324 -
all-1404 -
obs--97.43 %

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