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- PDB-6gug: Siderophore hydrolase EstB mutant S148A from Aspergillus fumigatus -

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Basic information

Entry
Database: PDB / ID: 6gug
TitleSiderophore hydrolase EstB mutant S148A from Aspergillus fumigatus
ComponentsSiderophore esterase IroE-like, putative
KeywordsHYDROLASE / alpha/beta-hydrolase / siderophore / hydrolysis / fungi
Function / homology: / siderophore-iron import into cell / Esterase-like / Putative esterase / hydrolase activity, acting on ester bonds / Alpha/Beta hydrolase fold / Hydrolases; Acting on ester bonds / cytoplasm / Siderophore triacetylfusarinine C esterase
Function and homology information
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsEcker, F. / Haas, H. / Groll, M. / Huber, E.M.
Funding support Germany, Austria, 2items
OrganizationGrant numberCountry
German Research FoundationGR 1861/8-1 Germany
Austrian Science FundFWF I 1346-B21 Austria
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Iron Scavenging in Aspergillus Species: Structural and Biochemical Insights into Fungal Siderophore Esterases.
Authors: Ecker, F. / Haas, H. / Groll, M. / Huber, E.M.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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

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Assembly

Deposited unit
A: Siderophore esterase IroE-like, putative
B: Siderophore esterase IroE-like, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,06210
Polymers65,3182
Non-polymers7458
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-66 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.790, 92.360, 130.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Siderophore esterase IroE-like, putative


Mass: 32658.873 Da / Num. of mol.: 2 / Mutation: S148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: AFUA_3G03660 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WF29
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.0 1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→45 Å / Num. obs: 113283 / % possible obs: 95.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.3
Reflection shellResolution: 1.45→1.55 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.2 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GUD

6gud


Resolution: 1.45→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.638 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18511 5659 5 %RANDOM
Rwork0.1662 ---
obs0.16714 107504 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.899 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--1.45 Å2-0 Å2
3----1.22 Å2
Refinement stepCycle: 1 / Resolution: 1.45→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4401 0 46 606 5053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194599
X-RAY DIFFRACTIONr_bond_other_d0.0010.024098
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.9456265
X-RAY DIFFRACTIONr_angle_other_deg0.86539486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1025562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4822.676213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.92415680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3171534
X-RAY DIFFRACTIONr_chiral_restr0.0560.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021027
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5152.1222230
X-RAY DIFFRACTIONr_mcbond_other0.5152.122229
X-RAY DIFFRACTIONr_mcangle_it0.5253.1762783
X-RAY DIFFRACTIONr_mcangle_other0.5253.1782784
X-RAY DIFFRACTIONr_scbond_it0.6032.3292369
X-RAY DIFFRACTIONr_scbond_other0.6012.3242361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5543.4113466
X-RAY DIFFRACTIONr_long_range_B_refined1.51126.4495373
X-RAY DIFFRACTIONr_long_range_B_other1.51126.455374
X-RAY DIFFRACTIONr_rigid_bond_restr0.47738697
X-RAY DIFFRACTIONr_sphericity_free16.0855380
X-RAY DIFFRACTIONr_sphericity_bonded4.55958786
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 400 -
Rwork0.295 7600 -
obs--93.46 %

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