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- PDB-6r1g: Crystal structure of Borrelia burgdorferi periplasmic protein BB0... -

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Basic information

Entry
Database: PDB / ID: 6r1g
TitleCrystal structure of Borrelia burgdorferi periplasmic protein BB0365 (IPLA7, p22)
ComponentsOuter surface 22 kDa lipoprotein
KeywordsMEMBRANE PROTEIN / periplasmic lipoprotein / Lyme disease
Function / homologycell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / membrane / TRIETHYLENE GLYCOL / Outer surface 22 kDa lipoprotein
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 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: Febs Lett. / Year: 2020
Title: Structural analysis of Borrelia burgdorferi periplasmic lipoprotein BB0365 involved in Lyme disease infection.
Authors: Brangulis, K. / Akopjana, I. / Petrovskis, I. / Kazaks, A. / Jekabsons, A. / Jaudzems, K. / Viksna, A. / Bertins, M. / Tars, K.
History
DepositionMar 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer surface 22 kDa lipoprotein
B: Outer surface 22 kDa lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0929
Polymers38,1232
Non-polymers9707
Water3,351186
1
A: Outer surface 22 kDa lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2773
Polymers19,0611
Non-polymers2162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer surface 22 kDa lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8166
Polymers19,0611
Non-polymers7545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.650, 63.470, 61.210
Angle α, β, γ (deg.)90.000, 111.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer surface 22 kDa lipoprotein / Antigen IPLA7


Mass: 19061.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first four 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: p22, BB_0365 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CL67
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M Na acetate 0.1 M Tris pH 8.5 35% PEG 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.94934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94934 Å / Relative weight: 1
ReflectionResolution: 1.55→47.22 Å / Num. obs: 50688 / % possible obs: 96.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 18.9
Reflection shellResolution: 1.55→1.63 Å / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 7281 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
SCALAdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→47.22 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.302 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.071
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 2536 5 %RANDOM
Rwork0.1753 ---
obs0.1761 48130 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.92 Å2 / Biso mean: 22.249 Å2 / Biso min: 10.21 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.55→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2344 0 58 186 2588
Biso mean--40.43 30.58 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132455
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172318
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.6323289
X-RAY DIFFRACTIONr_angle_other_deg1.4871.5825426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9065300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77225.455110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00515443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.201152
X-RAY DIFFRACTIONr_chiral_restr0.1020.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022663
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 211 -
Rwork0.229 3471 -
all-3682 -
obs--95.59 %

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