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- PDB-6ba9: YbtT - Type II thioesterase from Yersiniabactin NRPS/PKS biosynth... -

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Basic information

Entry
Database: PDB / ID: 6ba9
TitleYbtT - Type II thioesterase from Yersiniabactin NRPS/PKS biosynthetic pathway- S89A mutant
ComponentsIron aquisition yersiniabactin synthesis enzyme, YbtT
KeywordsHYDROLASE / Thioesterase / non-ribosomal peptide synthesis / sideraphore synthesis / yersiniabactin
Function / homologyThioesterase type II, NRPS/PKS/S-FAS / Hydrolases; Acting on ester bonds; Thioester hydrolases / Thioesterase / Thioesterase domain / biosynthetic process / Alpha/Beta hydrolase fold / hydrolase activity / Siderophore biosynthesis thioesterase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBrett, T.J. / Kober, D.L. / Ohlemacher, S.I. / Henderson, J.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK099534 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL119813 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: YbtT is a low-specificity type II thioesterase that maintains production of the metallophore yersiniabactin in pathogenic enterobacteria.
Authors: Ohlemacher, S.I. / Xu, Y. / Kober, D.L. / Malik, M. / Nix, J.C. / Brett, T.J. / Henderson, J.P.
History
DepositionOct 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron aquisition yersiniabactin synthesis enzyme, YbtT


Theoretical massNumber of molelcules
Total (without water)29,3951
Polymers29,3951
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.450, 82.450, 82.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21A-441-

HOH

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Components

#1: Protein Iron aquisition yersiniabactin synthesis enzyme, YbtT / Surfactin synthase thioesterase subunit / Thioesterase / Yersiniabactin siderophore biosynthetic ...Surfactin synthase thioesterase subunit / Thioesterase / Yersiniabactin siderophore biosynthetic protein / Yersiniabactin synthetase / thioesterase component


Mass: 29395.311 Da / Num. of mol.: 1 / Mutation: S89A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: irp4, srfAD, A4T40_14730, AML07_28155, AUS26_21405, AW106_20985, ECONIH1_11380, ERS085406_04094, ERS150876_03959, FORC28_2175, MS6198_22290, SK85_02209, WM48_10340
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 DE3
References: UniProt: A0A061LQM0, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.37 Å3/Da / Density % sol: 48.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 200 mM di-ammonium hydrogen citrate, 21% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 2, 2017
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→58.3 Å / Num. obs: 55628 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 16.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Net I/σ(I): 22.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 5 % / Rmerge(I) obs: 1.865 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2396 / CC1/2: 0.303 / Rpim(I) all: 1.109 / Rrim(I) all: 2.077 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QMW

3qmw


Resolution: 1.4→47.524 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19
RfactorNum. reflection% reflection
Rfree0.1796 2790 5.03 %
Rwork0.166 --
obs0.1667 55425 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→47.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 0 298 2253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082013
X-RAY DIFFRACTIONf_angle_d0.9742747
X-RAY DIFFRACTIONf_dihedral_angle_d14.687722
X-RAY DIFFRACTIONf_chiral_restr0.077297
X-RAY DIFFRACTIONf_plane_restr0.007363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.42420.37651020.33312214X-RAY DIFFRACTION84
1.4242-1.45010.30531500.3012398X-RAY DIFFRACTION92
1.4501-1.4780.2751270.27942541X-RAY DIFFRACTION97
1.478-1.50810.26451380.2492610X-RAY DIFFRACTION99
1.5081-1.54090.28041310.21782618X-RAY DIFFRACTION100
1.5409-1.57680.21541630.20732623X-RAY DIFFRACTION100
1.5768-1.61620.21411050.1882691X-RAY DIFFRACTION100
1.6162-1.65990.19691310.1742630X-RAY DIFFRACTION100
1.6599-1.70870.21311310.17282660X-RAY DIFFRACTION100
1.7087-1.76390.18011490.1732637X-RAY DIFFRACTION100
1.7639-1.82690.22511130.16892668X-RAY DIFFRACTION100
1.8269-1.90010.15721120.1562683X-RAY DIFFRACTION100
1.9001-1.98660.16781480.15032633X-RAY DIFFRACTION100
1.9866-2.09130.16521380.14592680X-RAY DIFFRACTION100
2.0913-2.22230.1521910.13852629X-RAY DIFFRACTION100
2.2223-2.39390.14881290.1432689X-RAY DIFFRACTION100
2.3939-2.63480.17361470.14882698X-RAY DIFFRACTION100
2.6348-3.0160.1721780.15942679X-RAY DIFFRACTION100
3.016-3.79960.15971500.15512748X-RAY DIFFRACTION100
3.7996-47.55120.17361570.16422906X-RAY DIFFRACTION100

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