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- PDB-2g8c: Atomic-resolution crystal structure of Borrelia burgdorferi OspA ... -

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Basic information

Entry
Database: PDB / ID: 2g8c
TitleAtomic-resolution crystal structure of Borrelia burgdorferi OspA via surface entropy reduction
Componentsouter surface protein A
KeywordsLIPID BINDING PROTEIN / beta sheet
Function / homology
Function and homology information


cell outer membrane / cell surface / membrane
Similarity search - Function
C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Beta Barrel ...C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Outer surface protein A / Outer surface protein A
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsMakabe, K. / Tereshko, V. / Koide, S.
CitationJournal: Protein Sci. / Year: 2006
Title: Atomic-resolution crystal structure of Borrelia burgdorferi outer surface protein A via surface engineering.
Authors: Makabe, K. / Tereshko, V. / Gawlak, G. / Yan, S. / Koide, S.
History
DepositionMar 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
O: outer surface protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8534
Polymers26,3951
Non-polymers4583
Water7,260403
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.224, 54.628, 66.459
Angle α, β, γ (deg.)90.00, 100.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein outer surface protein A


Mass: 26395.469 Da / Num. of mol.: 1
Mutation: E37S, E45S, K46S, K48A, K60A, K64S, K83A, K104S, K107S, E196A, K239S, E240S, K254S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14013, UniProt: P0CL66*PLUS
#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 30% PEG400, 0.1M imidazole, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→20 Å / Num. all: 82636 / Num. obs: 82636 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 17.76
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.04 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OSP, O chain

1osp


Resolution: 1.15→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.018 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17996 4113 5 %RANDOM
Rwork0.15364 ---
obs0.15498 78535 99.63 %-
all-78535 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.183 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.04 Å2
2--1.01 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 26 403 2298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221913
X-RAY DIFFRACTIONr_bond_other_d0.0060.021791
X-RAY DIFFRACTIONr_angle_refined_deg1.78422588
X-RAY DIFFRACTIONr_angle_other_deg0.91434243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95827.70561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55715383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.095153
X-RAY DIFFRACTIONr_chiral_restr0.1180.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022080
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
X-RAY DIFFRACTIONr_nbd_refined0.2080.2298
X-RAY DIFFRACTIONr_nbd_other0.1920.21654
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2949
X-RAY DIFFRACTIONr_nbtor_other0.0860.21107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2223
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.120.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.05721318
X-RAY DIFFRACTIONr_mcbond_other0.9072524
X-RAY DIFFRACTIONr_mcangle_it2.62332036
X-RAY DIFFRACTIONr_scbond_it2.3762720
X-RAY DIFFRACTIONr_scangle_it3.2013542
X-RAY DIFFRACTIONr_rigid_bond_restr1.37833924
X-RAY DIFFRACTIONr_sphericity_free6.033403
X-RAY DIFFRACTIONr_sphericity_bonded3.37233686
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.191 323 -
Rwork0.183 5745 -
obs--99.77 %

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