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- PDB-3ec5: The crystal structure of Thioflavin-T (ThT) binding OspA mutant -

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Basic information

Entry
Database: PDB / ID: 3ec5
TitleThe crystal structure of Thioflavin-T (ThT) binding OspA mutant
ComponentsOuter Surface Protein A
KeywordsMEMBRANE PROTEIN / single-layer beta-sheet
Function / homology
Function and homology information


cell outer 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 / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Outer Surface Protein A
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBiancalana, M. / Makabe, K. / Koide, A. / Koide, S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies
Authors: Biancalana, M. / Makabe, K. / Koide, A. / Koide, S.
History
DepositionAug 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9273
Polymers34,5391
Non-polymers3882
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.073, 35.876, 92.606
Angle α, β, γ (deg.)90.00, 105.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer Surface Protein A


Mass: 34538.527 Da / Num. of mol.: 1
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) / References: UniProt: D0VWU8*PLUS
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 40% PEG-400, 2% glycerol, 0.85M Tris-Cl, 0.25M (NH4)2SO4, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 23, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 34301 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.087
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 1.74 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OY7

2oy7


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.657 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27388 3435 10 %RANDOM
Rwork0.22311 ---
obs0.22808 30820 99.77 %-
all-30820 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.558 Å2
Baniso -1Baniso -2Baniso -3
1-4.24 Å20 Å2-0.11 Å2
2---2.1 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 26 249 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222461
X-RAY DIFFRACTIONr_bond_other_d0.0020.021681
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9973307
X-RAY DIFFRACTIONr_angle_other_deg2.27734186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95426.78287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40415492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22155
X-RAY DIFFRACTIONr_chiral_restr0.0840.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022666
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02418
X-RAY DIFFRACTIONr_nbd_refined0.2090.2414
X-RAY DIFFRACTIONr_nbd_other0.2160.21728
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21179
X-RAY DIFFRACTIONr_nbtor_other0.0940.21440
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.220
X-RAY DIFFRACTIONr_mcbond_it1.2331.52033
X-RAY DIFFRACTIONr_mcbond_other0.1011.5658
X-RAY DIFFRACTIONr_mcangle_it1.09622545
X-RAY DIFFRACTIONr_scbond_it2.43831012
X-RAY DIFFRACTIONr_scangle_it3.3794.5757
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 255 -
Rwork0.299 2191 -
obs--97.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.43530.0944-0.20232.3004-0.51311.7207-0.0762-0.14710.0148-0.3135-0.0368-0.03850.16860.07170.113-0.163-0.0024-0.03830.0404-0.00010.0249.67036.393833.5718
20.4167-0.004-0.18681.43280.95522.8505-0.0120.05520.04350.0568-0.0756-0.21080.0259-0.06030.0876-0.00090.00390.0092-0.14770.0067-0.10816.690910.22761.3758
30.24780.17430.05491.5208-0.19031.9094-0.08120.0405-0.05550.03210.09530.1850.2015-0.0165-0.0141-0.1145-0.01460.03710.05630.02170.03316.1551-5.3394-31.8819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA28 - 1186 - 96
2X-RAY DIFFRACTION2AA119 - 20997 - 187
3X-RAY DIFFRACTION3AA210 - 342188 - 320

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