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- PDB-6qo1: Crystal structure of Borrelia (Borreliella) burgdorferi outer sur... -

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Basic information

Entry
Database: PDB / ID: 6qo1
TitleCrystal structure of Borrelia (Borreliella) burgdorferi outer surface protein BBA69
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 B31 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 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
DepositionFeb 12, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative surface protein
D: Putative surface protein
B: Putative surface protein
C: Putative surface protein


Theoretical massNumber of molelcules
Total (without water)89,8064
Polymers89,8064
Non-polymers00
Water1,17165
1
A: Putative surface protein


Theoretical massNumber of molelcules
Total (without water)22,4511
Polymers22,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Putative surface protein


Theoretical massNumber of molelcules
Total (without water)22,4511
Polymers22,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Putative surface protein


Theoretical massNumber of molelcules
Total (without water)22,4511
Polymers22,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Putative surface protein


Theoretical massNumber of molelcules
Total (without water)22,4511
Polymers22,4511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.262, 96.086, 67.348
Angle α, β, γ (deg.)90.000, 105.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative surface protein


Mass: 22451.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: First 4 residues (GAMG) are remnants from the expression tag.
Source: (gene. exp.) Borrelia burgdorferi B31 (bacteria) / Gene: BB_A69 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O50958
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
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

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.110.979724
SYNCHROTRONMAX II I911-321
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELJan 24, 2019
MARMOSAIC 225 mm CCD2CCDFeb 16, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9797241
211
ReflectionResolution: 2.25→48.04 Å / Num. obs: 39086 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.5
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 3574 / % possible all: 100

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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: 2.25→40.62 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.93 / SU B: 19.754 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 1983 5.1 %RANDOM
Rwork0.1728 ---
obs0.1766 37109 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 362.85 Å2 / Biso mean: 36.206 Å2 / Biso min: 13.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.01 Å2
2---0.03 Å20 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 2.25→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6136 0 0 65 6201
Biso mean---46.54 -
Num. residues----744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136196
X-RAY DIFFRACTIONr_bond_other_d0.0040.0175948
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.6458304
X-RAY DIFFRACTIONr_angle_other_deg1.3231.58913944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0695740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30625.882340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.316151336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8771520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026712
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021076
X-RAY DIFFRACTIONr_rigid_bond_restr19.593312144
LS refinement shellResolution: 2.248→2.306 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 136 -
Rwork0.187 2668 -
all-2804 -
obs--97.43 %

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