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- PDB-3eex: The crystal structure of OspA mutant -

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Basic information

Entry
Database: PDB / ID: 3eex
TitleThe crystal structure of OspA mutant
ComponentsOuter Surface Protein A
KeywordsMEMBRANE PROTEIN / beta-sheet
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsMakabe, K. / Biancalana, M. / Koide, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Minimalist design of water-soluble cross-{beta} architecture.
Authors: Biancalana, M. / Makabe, K. / Koide, S.
History
DepositionSep 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer Surface Protein A
B: Outer Surface Protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7045
Polymers68,8572
Non-polymers8473
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-16 kcal/mol
Surface area33180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.502, 82.401, 109.428
Angle α, β, γ (deg.)90.00, 91.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer Surface Protein A


Mass: 34428.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM

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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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 34% PEG400, 0.1M Tris-HCl pH 9, protein 20.2 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 22424 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.094
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.33 / Num. unique all: 2258 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3CKA

3cka


Resolution: 2.49→20 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.876 / SU B: 28.187 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.556 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29875 2264 10.1 %RANDOM
Rwork0.26211 ---
obs0.26578 20097 98.67 %-
all-20097 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.185 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å20 Å20.02 Å2
2---5.67 Å20 Å2
3---2.71 Å2
Refinement stepCycle: LAST / Resolution: 2.49→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 18 0 4794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224831
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.9876482
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7835630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8326.667174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.61615962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5571510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023370
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.21771
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23217
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2179
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8341.53194
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.12125028
X-RAY DIFFRACTIONr_scbond_it1.69831795
X-RAY DIFFRACTIONr_scangle_it2.8464.51454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 151 -
Rwork0.356 1418 -
obs--95.96 %

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