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- PDB-6e6s: 1.45 A resolution structure of the C-terminally truncated [2Fe-2S... -

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Basic information

Entry
Database: PDB / ID: 6e6s
Title1.45 A resolution structure of the C-terminally truncated [2Fe-2S] ferredoxin (Bfd) R26E/K46Y mutant from Pseudomonas aeruginosa
ComponentsBacterioferritin-associated ferredoxin
KeywordsELECTRON TRANSPORT / IRON MOBILIZATION / [2Fe-2S] ferredoxin / Bfd / anion binding site
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
BFD-like [2Fe-2S]-binding domain / : / BFD-like [2Fe-2S] binding domain / BFD-like [2Fe-2S]-binding domain / BFD-like [2Fe-2S]-binding domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Bacterioferritin-associated ferredoxin / Bacterioferritin-associated ferredoxin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsLovell, S. / Wijerathne, H. / Battaile, K.P. / Yao, H. / Wang, Y. / Rivera, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125529 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110761 United States
CitationJournal: Biochemistry / Year: 2018
Title: Bfd, a New Class of [2Fe-2S] Protein That Functions in Bacterial Iron Homeostasis, Requires a Structural Anion Binding Site.
Authors: Wijerathne, H. / Yao, H. / Wang, Y. / Lovell, S. / Battaile, K.P. / Rivera, M.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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: Bacterioferritin-associated ferredoxin
B: Bacterioferritin-associated ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7024
Polymers12,3502
Non-polymers3522
Water1,60389
1
A: Bacterioferritin-associated ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3512
Polymers6,1751
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bacterioferritin-associated ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3512
Polymers6,1751
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.186, 46.192, 48.846
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bacterioferritin-associated ferredoxin / BFD-like [2Fe-2S] binding domain protein / Bacterioferritin-associated ferredoxin


Mass: 6174.949 Da / Num. of mol.: 2 / Fragment: M1-L56 / Mutation: R26E, C43S, K46Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: bfd, AO896_12000, AO964_01120, AOY09_04877, C8257_08100, CAZ03_03910, CAZ10_19915, CGU42_05470, CSB93_2785, PAERUG_E15_London_28_01_14_09195, PAMH19_1562, RW109_RW109_02290
Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Variant (production host): ARCTIC EXPRESS RIL / References: UniProt: A0A069Q647, UniProt: Q9HY80*PLUS
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 1.97 Å3/Da / Density % sol: 37.64 % / Mosaicity: 0.1 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.5 M NaCl, 10% (v/v) ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→48.85 Å / Num. obs: 17875 / % possible obs: 99.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.8 / Num. measured all: 113397
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.45-1.476.60.898700.862199.9
7.94-48.855.30.0261471199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.5 Å30.93 Å
Translation1.5 Å30.93 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E6K

4e6k


Resolution: 1.45→33.562 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.06 / Phase error: 22.31
RfactorNum. reflection% reflection
Rfree0.1916 762 4.28 %
Rwork0.1604 --
obs0.1616 17806 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.92 Å2 / Biso mean: 24.2948 Å2 / Biso min: 15.13 Å2
Refinement stepCycle: final / Resolution: 1.45→33.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms828 0 8 89 925
Biso mean--24.57 32.69 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009862
X-RAY DIFFRACTIONf_angle_d1.5161172
X-RAY DIFFRACTIONf_chiral_restr0.068138
X-RAY DIFFRACTIONf_plane_restr0.006155
X-RAY DIFFRACTIONf_dihedral_angle_d12.318314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.5620.23321730.202933313504100
1.562-1.71910.2171850.156633403525100
1.7191-1.96790.2151560.140333823538100
1.9679-2.47920.18991190.15353379349898
2.4792-33.57070.17351290.16436123741100

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