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- PDB-6win: Type 6 secretion amidase effector 2 (Tae2) -

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Basic information

Entry
Database: PDB / ID: 6win
TitleType 6 secretion amidase effector 2 (Tae2)
ComponentsType 6 secretion amidase effector 2
KeywordsANTIMICROBIAL PROTEIN / amidase / toxin / peptidoglycan hydrolase
Function / homology: / BPSL0067 family protein
Function and homology information
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsChou, S. / Radkov, A.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI132851 United States
CitationJournal: Cell / Year: 2020
Title: Ticks Resist Skin Commensals with Immune Factor of Bacterial Origin.
Authors: Hayes, B.M. / Radkov, A.D. / Yarza, F. / Flores, S. / Kim, J. / Zhao, Z. / Lexa, K.W. / Marnin, L. / Biboy, J. / Bowcut, V. / Vollmer, W. / Pedra, J.H.F. / Chou, S.
History
DepositionApr 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type 6 secretion amidase effector 2


Theoretical massNumber of molelcules
Total (without water)15,9871
Polymers15,9871
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.318, 46.032, 38.923
Angle α, β, γ (deg.)90.000, 104.712, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Type 6 secretion amidase effector 2


Mass: 15986.507 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: STY0300, t2586 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Z969
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 32.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1M sodium citrate 0.1M MES pH 6.6 4% formamide

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Data collection

DiffractionMean temperature: 91 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97954 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.68→46.03 Å / Num. obs: 9246 / % possible obs: 70.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 20.74 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.039 / Rrim(I) all: 0.098 / Net I/σ(I): 16 / Num. measured all: 52864 / Scaling rejects: 1
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.989 / Num. measured all: 84 / Num. unique obs: 37 / CC1/2: 0.443 / Rpim(I) all: 0.757 / Rrim(I) all: 1.255 / Net I/σ(I) obs: 1.4 / % possible all: 5.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
ELVESdata scaling
PDB_EXTRACT3.25data extraction
ELVESdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→37.65 Å / SU ML: 0.2311 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 26.3295
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2238 712 10 %
Rwork0.1745 6408 -
obs0.1795 7120 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.85 Å2
Refinement stepCycle: LAST / Resolution: 2.05→37.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 0 87 1196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721140
X-RAY DIFFRACTIONf_angle_d0.81121549
X-RAY DIFFRACTIONf_chiral_restr0.056159
X-RAY DIFFRACTIONf_plane_restr0.0043206
X-RAY DIFFRACTIONf_dihedral_angle_d29.6374153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.210.28811320.19491196X-RAY DIFFRACTION92.09
2.21-2.430.23511430.18581284X-RAY DIFFRACTION99.65
2.43-2.780.26181440.18831303X-RAY DIFFRACTION99.59
2.78-3.50.23351440.1811289X-RAY DIFFRACTION99.79
3.51-37.650.18311490.15581336X-RAY DIFFRACTION99.93

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