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- PDB-6roc: Crystal structure of Borrelia burgdorferi outer surface protein B... -

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Basic information

Entry
Database: PDB / ID: 6roc
TitleCrystal structure of Borrelia burgdorferi outer surface protein BBA69, mutant Leu214Met (Se-Met data)
ComponentsPutative surface protein
KeywordsMEMBRANE PROTEIN / Outer surface protein / PFam54
Function / homologyBorrelia lipoprotein paralogus family 54/60 / Borrelia Bbcrasp-1 domain containing protein / membrane / Surface protein
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsBrangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Tars, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.2/VIAA/1/16/144 Latvia
CitationJournal: Ticks Tick Borne Dis / Year: 2019
Title: Crystal structure of Borrelia burgdorferi outer surface protein BBA69 in comparison to the paralogous protein CspA.
Authors: Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Tars, K.
History
DepositionMay 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)44,9392
Polymers44,9392
Non-polymers00
Water00
1
A: Putative surface protein


Theoretical massNumber of molelcules
Total (without water)22,4691
Polymers22,4691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative surface protein


Theoretical massNumber of molelcules
Total (without water)22,4691
Polymers22,4691
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.970, 110.552, 61.695
Angle α, β, γ (deg.)90.000, 126.830, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative surface protein


Mass: 22469.486 Da / Num. of mol.: 2 / Mutation: Leu214 mutated to Met
Source method: isolated from a genetically manipulated source
Details: First 4 residues (GAMG) are remnants from the expression tag.
Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_A69 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50958

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1M (NH4)2SO4 0.1M Tris pH 8.0 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.574
11-H, -K, H+L20.426
ReflectionResolution: 2.9→52.19 Å / Num. obs: 8521 / % possible obs: 96.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.2
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 1374 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→52.19 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 19.912 / SU ML: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 426 5 %RANDOM
Rwork0.1987 ---
obs0.2021 8094 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 162.17 Å2 / Biso mean: 70.733 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å214.18 Å2
2---0.77 Å20 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 2.9→52.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 0 0 2998
Num. residues----365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133015
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172926
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.6444035
X-RAY DIFFRACTIONr_angle_other_deg1.1611.596853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2715359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97325.802162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87315654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9091510
X-RAY DIFFRACTIONr_chiral_restr0.0540.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023239
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02519
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 15 -
Rwork0.199 576 -
all-591 -
obs--92.06 %

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