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- PDB-6gur: Siderophore hydrolase EstB from Aspergillus fumigatus in complex ... -

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Basic information

Entry
Database: PDB / ID: 6gur
TitleSiderophore hydrolase EstB from Aspergillus fumigatus in complex with TAFC
ComponentsSiderophore triacetylfusarinine C esterase
KeywordsHYDROLASE / alpha/beta-hydrolase / siderophore / hydrolysis / fungi
Function / homology
Function and homology information


siderophore-iron import into cell / hydrolase activity, acting on ester bonds / Hydrolases; Acting on ester bonds / cytoplasm
Similarity search - Function
: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
CARBONATE ION / : / Chem-FN8 / Siderophore triacetylfusarinine C esterase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Siderophore triacetylfusarinine C esterase
B: Siderophore triacetylfusarinine C esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,91314
Polymers65,3502
Non-polymers1,56312
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homodimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-47 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.740, 89.990, 129.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Siderophore triacetylfusarinine C esterase


Mass: 32674.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: estB, AFUA_3G03660 / Production host: Escherichia coli (E. coli)
References: UniProt: Q4WF29, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 187 molecules

#2: Chemical ChemComp-FN8 / (~{Z})-5-[(1~{S},2~{S})-2-acetamido-1-oxidanyl-5-[oxidanyl(propanoyl)amino]pentoxy]-~{N},3-dimethyl-~{N}-oxidanyl-pent-2-enamide


Mass: 389.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H31N3O7
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5 0.65 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: Jun 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45 Å / Num. obs: 37038 / % possible obs: 96.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.8
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.5 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GUD

6gud


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 13.58 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23793 1846 5 %RANDOM
Rwork0.1981 ---
obs0.20004 35075 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.906 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--3.3 Å2-0 Å2
3----2.05 Å2
Refinement stepCycle: 1 / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 99 175 4722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0144681
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174046
X-RAY DIFFRACTIONr_angle_refined_deg0.871.6676364
X-RAY DIFFRACTIONr_angle_other_deg0.6991.6589470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2875559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9820.88250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16415690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1921535
X-RAY DIFFRACTIONr_chiral_restr0.0330.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02931
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_it0.8564.4472242
X-RAY DIFFRACTIONr_mcbond_other0.8544.4452241
X-RAY DIFFRACTIONr_mcangle_it1.2576.6592796
X-RAY DIFFRACTIONr_mcangle_other1.2576.6612797
X-RAY DIFFRACTIONr_scbond_it0.7424.6452439
X-RAY DIFFRACTIONr_scbond_other0.7364.6392433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0716.8883562
X-RAY DIFFRACTIONr_long_range_B_refined2.53351.4945235
X-RAY DIFFRACTIONr_long_range_B_other2.39251.3085198
X-RAY DIFFRACTIONr_rigid_bond_restr0.18438727
X-RAY DIFFRACTIONr_sphericity_free26.623572
X-RAY DIFFRACTIONr_sphericity_bonded16.74558699
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 133 -
Rwork0.28 2540 -
obs--98.31 %

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