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- PDB-6fx6: Thioester domain of the Staphylococcus aureus TIE protein -

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Basic information

Entry
Database: PDB / ID: 6fx6
TitleThioester domain of the Staphylococcus aureus TIE protein
ComponentsSaTIE-TED
KeywordsUNKNOWN FUNCTION / LPXTG-anchored / surface protein / thioester domain / TIE protein
Function / homologyThioester domain / Thioester domain / ACETATE ION / SaTIE-TED
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsMiller, O.K. / Banfield, M.J. / Schwarz-Linek, U.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K001485 United Kingdom
Royal Society of Edinburgh United Kingdom
Citation
Journal: Protein Sci. / Year: 2018
Title: A new structural class of bacterial thioester domains reveals a slipknot topology.
Authors: Miller, O.K. / Banfield, M.J. / Schwarz-Linek, U.
#1: Journal: Elife / Year: 2015
Title: An internal thioester in a pathogen surface protein mediates covalent host binding.
Authors: Walden, M. / Edwards, J.M. / Dziewulska, A.M. / Bergmann, R. / Saalbach, G. / Kan, S.Y. / Miller, O.K. / Weckener, M. / Jackson, R.J. / Shirran, S.L. / Botting, C.H. / Florence, G.J. / ...Authors: Walden, M. / Edwards, J.M. / Dziewulska, A.M. / Bergmann, R. / Saalbach, G. / Kan, S.Y. / Miller, O.K. / Weckener, M. / Jackson, R.J. / Shirran, S.L. / Botting, C.H. / Florence, G.J. / Rohde, M. / Banfield, M.J. / Schwarz-Linek, U.
History
DepositionMar 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_data_processing_status ...atom_site / pdbx_data_processing_status / pdbx_nonpoly_scheme / pdbx_solvent_atom_site_mapping / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_solvent_atom_site_mapping.auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SaTIE-TED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7295
Polymers28,4801
Non-polymers2494
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration indicates monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-37 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.029, 73.612, 74.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SaTIE-TED


Mass: 28479.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pEHisTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3F2YM24*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.12 Å3/Da / Density % sol: 42.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 2000 monomethyl ether, Tris, zinc acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.25→74.65 Å / Num. obs: 12054 / % possible obs: 99.8 % / Redundancy: 26.8 % / Biso Wilson estimate: 45.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Net I/σ(I): 20.5
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 21.1 % / Rmerge(I) obs: 1.067 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1084 / CC1/2: 0.873 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→74.65 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 15.367 / SU ML: 0.196 / SU R Cruickshank DPI: 0.342 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.233
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 617 5.1 %RANDOM
Rwork0.2021 ---
obs0.2043 11395 99.77 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.63 Å2 / Biso mean: 45.254 Å2 / Biso min: 16.93 Å2
Baniso -1Baniso -2Baniso -3
1-5.49 Å20 Å20 Å2
2---4.71 Å20 Å2
3----0.78 Å2
Refinement stepCycle: final / Resolution: 2.25→74.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1877 0 10 61 1948
Biso mean--61.85 39.1 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191927
X-RAY DIFFRACTIONr_bond_other_d0.0010.021820
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9492605
X-RAY DIFFRACTIONr_angle_other_deg0.82234231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22425.40287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63215340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.66157
X-RAY DIFFRACTIONr_chiral_restr0.0680.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02370
LS refinement shellResolution: 2.25→2.308 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 35 -
Rwork0.313 823 -
all-858 -
obs--97.17 %
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)
13.3592-0.3529-0.08635.29632.61084.9418-0.0205-0.1614-0.13760.3692-0.2860.48990.2727-0.27620.30650.0607-0.04490.01720.0617-0.01150.0604-3.7055-9.377725.426
21.39420.831.47562.93562.2244.7264-0.05330.1619-0.0421-0.044-0.04220.00730.09160.04380.09550.013-0.00550.01440.04230.01870.0652-5.0509-26.92461.308
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 134
2X-RAY DIFFRACTION2A135 - 240

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