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- PDB-6gun: Siderophore hydrolase EstB from Aspergillus nidulans -

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Basic information

Entry
Database: PDB / ID: 6gun
TitleSiderophore hydrolase EstB from Aspergillus nidulans
ComponentsEstB from Aspergillus nidulans
KeywordsHYDROLASE / alpha/beta-hydrolase / siderophore / hydrolysis / fungi
Function / homology: / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold / EstB from Aspergillus nidulans
Function and homology information
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

Downloads & links

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Assembly

Deposited unit
A: EstB from Aspergillus nidulans
B: EstB from Aspergillus nidulans
C: EstB from Aspergillus nidulans
D: EstB from Aspergillus nidulans
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6686
Polymers138,4844
Non-polymers1842
Water8,629479
1
A: EstB from Aspergillus nidulans
B: EstB from Aspergillus nidulans
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3343
Polymers69,2422
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-18 kcal/mol
Surface area25120 Å2
MethodPISA
2
D: EstB from Aspergillus nidulans
hetero molecules

C: EstB from Aspergillus nidulans


Theoretical massNumber of molelcules
Total (without water)69,3343
Polymers69,2422
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area4540 Å2
ΔGint-18 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.460, 72.050, 108.100
Angle α, β, γ (deg.)90.00, 111.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
EstB from Aspergillus nidulans


Mass: 34620.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3F2YM31*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0 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: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. obs: 82011 / % possible obs: 97.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 10
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4

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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→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 13.384 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R Free: 0.171 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23429 4089 5 %RANDOM
Rwork0.19498 ---
obs0.19696 77699 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.114 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å2-0.85 Å2
2--0.97 Å20 Å2
3---1.04 Å2
Refinement stepCycle: 1 / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9312 0 12 482 9806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0149584
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178312
X-RAY DIFFRACTIONr_angle_refined_deg0.7611.65412996
X-RAY DIFFRACTIONr_angle_other_deg0.6851.63219495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61251164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.22520.344553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.583151513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5441592
X-RAY DIFFRACTIONr_chiral_restr0.0330.21167
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021894
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_it0.8595.1164680
X-RAY DIFFRACTIONr_mcbond_other0.8595.1154679
X-RAY DIFFRACTIONr_mcangle_it1.2797.6655836
X-RAY DIFFRACTIONr_mcangle_other1.2797.6665837
X-RAY DIFFRACTIONr_scbond_it0.7075.284904
X-RAY DIFFRACTIONr_scbond_other0.7075.284904
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0197.8667161
X-RAY DIFFRACTIONr_long_range_B_refined2.32358.64110889
X-RAY DIFFRACTIONr_long_range_B_other2.18958.52610799
X-RAY DIFFRACTIONr_rigid_bond_restr0.172317896
X-RAY DIFFRACTIONr_sphericity_free27.3475216
X-RAY DIFFRACTIONr_sphericity_bonded25.229517902
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 298 -
Rwork0.326 5667 -
obs--98.43 %

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