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- PDB-6guo: Siderophore hydrolase EstA from Aspergillus nidulans -

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Basic information

Entry
Database: PDB / ID: 6guo
TitleSiderophore hydrolase EstA from Aspergillus nidulans
ComponentsPutative siderophore-degrading esterase (Eurofung)
KeywordsHYDROLASE / alpha/beta-hydrolase / siderophore / hydrolysis / fungi
Function / homology: / Esterase-like / Putative esterase / hydrolase activity, acting on ester bonds / Alpha/Beta hydrolase fold / TRIETHYLENE GLYCOL / Siderophore-degrading esterase (Eurofung)
Function and homology information
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.3May 8, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative siderophore-degrading esterase (Eurofung)
B: Putative siderophore-degrading esterase (Eurofung)
C: Putative siderophore-degrading esterase (Eurofung)
D: Putative siderophore-degrading esterase (Eurofung)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,04718
Polymers134,6914
Non-polymers1,35614
Water19,0241056
1
A: Putative siderophore-degrading esterase (Eurofung)
B: Putative siderophore-degrading esterase (Eurofung)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,08810
Polymers67,3462
Non-polymers7438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-67 kcal/mol
Surface area25070 Å2
MethodPISA
2
C: Putative siderophore-degrading esterase (Eurofung)
hetero molecules

D: Putative siderophore-degrading esterase (Eurofung)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9598
Polymers67,3462
Non-polymers6146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area6720 Å2
ΔGint-46 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.570, 236.190, 51.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Putative siderophore-degrading esterase (Eurofung) / EstA


Mass: 33672.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Gene: ANIA_07801 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5AV79
#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1056 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5 0.25 M NaCl 20 % PEG3350

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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: 1.75→45 Å / Num. obs: 129886 / % possible obs: 99 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.6
Reflection shellResolution: 1.75→1.85 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7

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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: 1.75→15 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.909 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.107 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20317 6478 5 %RANDOM
Rwork0.16317 ---
obs0.16517 123129 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.446 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å20 Å2
2--0.26 Å2-0 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9393 0 82 1063 10538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0199857
X-RAY DIFFRACTIONr_bond_other_d0.0020.028950
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.95513384
X-RAY DIFFRACTIONr_angle_other_deg0.881320746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24751233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60322.222450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.235151531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6631593
X-RAY DIFFRACTIONr_chiral_restr0.0630.21408
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022221
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_it1.4782.5284851
X-RAY DIFFRACTIONr_mcbond_other1.4782.5284850
X-RAY DIFFRACTIONr_mcangle_it1.7953.7816075
X-RAY DIFFRACTIONr_mcangle_other1.7953.7816076
X-RAY DIFFRACTIONr_scbond_it1.6122.8875006
X-RAY DIFFRACTIONr_scbond_other1.6122.8875006
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8854.27298
X-RAY DIFFRACTIONr_long_range_B_refined2.96130.77611281
X-RAY DIFFRACTIONr_long_range_B_other2.73430.29911059
X-RAY DIFFRACTIONr_rigid_bond_restr1.713318807
X-RAY DIFFRACTIONr_sphericity_free26.4265647
X-RAY DIFFRACTIONr_sphericity_bonded10.663518954
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 472 -
Rwork0.242 8975 -
obs--99.63 %

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