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- PDB-6gup: Siderophore hydrolase EstB from Aspergillus fumigatus -

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Basic information

Entry
Database: PDB / ID: 6gup
TitleSiderophore hydrolase EstB from Aspergillus fumigatus
ComponentsSiderophore biosynthesis lipase/esterase, putative
KeywordsHYDROLASE / alpha/beta-hydrolase / siderophore / hydrolysis / fungi
Function / homologyFusarinine C esterase SidJ / Protein of unknown function (DUF1749) / Alpha/Beta hydrolase fold / Hydrolases; Acting on ester bonds / hydrolase activity / Fusarinine C esterase sidJ
Function and homology information
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 biosynthesis lipase/esterase, putative
B: Siderophore biosynthesis lipase/esterase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1283
Polymers78,0362
Non-polymers921
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-21 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.930, 102.850, 65.060
Angle α, β, γ (deg.)90.00, 92.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Siderophore biosynthesis lipase/esterase, putative


Mass: 39017.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: AFUA_3G03390 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WF56
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 5.5 17% PEG 400

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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: Jun 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→45 Å / Num. obs: 53434 / % possible obs: 97.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.1
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.2 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 10.889 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.617 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24347 2666 5 %RANDOM
Rwork0.21114 ---
obs0.21274 50664 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å2-0 Å2-1.87 Å2
2---2.52 Å20 Å2
3---1.97 Å2
Refinement stepCycle: 1 / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5105 0 6 266 5377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195226
X-RAY DIFFRACTIONr_bond_other_d0.0020.024786
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.9657103
X-RAY DIFFRACTIONr_angle_other_deg0.888311116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4585654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7323.846221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97115853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5461531
X-RAY DIFFRACTIONr_chiral_restr0.0580.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021039
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_it1.3774.7962637
X-RAY DIFFRACTIONr_mcbond_other1.3734.7932636
X-RAY DIFFRACTIONr_mcangle_it1.4667.1713284
X-RAY DIFFRACTIONr_mcangle_other1.4667.1743285
X-RAY DIFFRACTIONr_scbond_it1.325.2062589
X-RAY DIFFRACTIONr_scbond_other1.3195.2062589
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2387.6733820
X-RAY DIFFRACTIONr_long_range_B_refined2.19358.0645839
X-RAY DIFFRACTIONr_long_range_B_other2.19358.0625839
X-RAY DIFFRACTIONr_rigid_bond_restr1.479310012
X-RAY DIFFRACTIONr_sphericity_free23.2125137
X-RAY DIFFRACTIONr_sphericity_bonded4.33510026
LS refinement shellResolution: 1.85→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 195 -
Rwork0.333 3701 -
obs--97.91 %

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