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- PDB-6e6q: 1.20 A resolution structure of the C-terminally truncated [2Fe-2S... -

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Basic information

Entry
Database: PDB / ID: 6e6q
Title1.20 A resolution structure of the C-terminally truncated [2Fe-2S] ferredoxin (Bfd) 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: 1.2 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)P30 GM110761 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)12,6904
Polymers12,3382
Non-polymers3522
Water1,892105
1
A: Bacterioferritin-associated ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,3452
Polymers6,1691
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)6,3452
Polymers6,1691
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)23.946, 49.710, 39.895
Angle α, β, γ (deg.)90.000, 96.850, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 6169.035 Da / Num. of mol.: 2 / Fragment: M1-L56 / Mutation: C43S
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 / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 105 / 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: 1.91 Å3/Da / Density % sol: 35.63 % / Mosaicity: 0.24 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% (v/v) 2-methyl-2,4-pentanediol, 100 mM sodium acetate, 20 mM CaCl2

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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: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→39.61 Å / Num. obs: 28905 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 11.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.3 / Num. measured all: 96242
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.2-1.223.20.63313770.766199.2
6.57-39.613.50.0431940.996199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.53 Å30.96 Å
Translation1.53 Å30.96 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
MOLREP10.2.35phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E6K

4e6k


Resolution: 1.2→39.61 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 15.56
RfactorNum. reflection% reflection
Rfree0.1483 1422 4.92 %
Rwork0.1214 --
obs0.1227 28874 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 48.53 Å2 / Biso mean: 15.6781 Å2 / Biso min: 8.34 Å2
Refinement stepCycle: final / Resolution: 1.2→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms842 0 8 105 955
Biso mean--10.91 29.54 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012879
X-RAY DIFFRACTIONf_angle_d1.6341189
X-RAY DIFFRACTIONf_chiral_restr0.08140
X-RAY DIFFRACTIONf_plane_restr0.007156
X-RAY DIFFRACTIONf_dihedral_angle_d19.331337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.24290.21951350.20382699283499
1.2429-1.29270.23161480.18632730287899
1.2927-1.35150.2071550.153627202875100
1.3515-1.42280.17191570.12727682925100
1.4228-1.51190.13881490.103327152864100
1.5119-1.62870.11631130.087727952908100
1.6287-1.79260.11411420.091627312873100
1.7926-2.05190.1511400.10392763290399
2.0519-2.58510.11881270.11232764289199
2.5851-39.63150.15111560.13342767292398

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