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- PDB-6nlf: 1.45 A resolution structure of apo BfrB from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6nlf
Title1.45 A resolution structure of apo BfrB from Pseudomonas aeruginosa
ComponentsFerroxidase
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / IRON BINDING / IRON MOBILIZATION / PROTEIN-PROTEIN INTERACTION
Function / homology
Function and homology information


iron ion sequestering activity / ferritin complex / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / iron ion binding / heme binding / cytosol
Similarity search - Function
Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Bacterioferritin signature. / Bacterioferritin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Bacterioferritin BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsLovell, S. / Punchi-Hewage, A. / Battaile, K.P. / Yao, H. / Nammalwar, B. / Gnanasekaran, K.K. / Bunce, R.A. / Reitz, A.B. / Rivera, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI125529 United States
National Science Foundation (NSF, United States)MCB1615767 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Small Molecule Inhibitors of the BfrB-Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity.
Authors: Punchi Hewage, A.N.D. / Yao, H. / Nammalwar, B. / Gnanasekaran, K.K. / Lovell, S. / Bunce, R.A. / Eshelman, K. / Phaniraj, S.M. / Lee, M.M. / Peterson, B.R. / Battaile, K.P. / Reitz, A.B. / Rivera, M.
History
DepositionJan 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: 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 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferroxidase
B: Ferroxidase
C: Ferroxidase
D: Ferroxidase
E: Ferroxidase
F: Ferroxidase
G: Ferroxidase
H: Ferroxidase
I: Ferroxidase
J: Ferroxidase
K: Ferroxidase
L: Ferroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,07915
Polymers222,96212
Non-polymers1173
Water44,1012448
1
A: Ferroxidase
B: Ferroxidase
C: Ferroxidase
D: Ferroxidase
E: Ferroxidase
F: Ferroxidase
G: Ferroxidase
H: Ferroxidase
I: Ferroxidase
J: Ferroxidase
K: Ferroxidase
L: Ferroxidase
hetero molecules

A: Ferroxidase
B: Ferroxidase
C: Ferroxidase
D: Ferroxidase
E: Ferroxidase
F: Ferroxidase
G: Ferroxidase
H: Ferroxidase
I: Ferroxidase
J: Ferroxidase
K: Ferroxidase
L: Ferroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)446,15930
Polymers445,92424
Non-polymers2356
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area68080 Å2
ΔGint-365 kcal/mol
Surface area134740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.727, 197.772, 204.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-246-

HOH

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Components

#1: Protein
Ferroxidase


Mass: 18580.168 Da / Num. of mol.: 12 / Fragment: BFRB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: bfrB, PA3531 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): ARCTIC EXPRESS RIL / References: UniProt: Q9HY79, ferroxidase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2448 / 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: 2.94 Å3/Da / Density % sol: 58.13 % / Mosaicity: 0.09 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 8% (w/v) PEG 8000, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→47.9 Å / Num. obs: 458281 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.8 / Num. measured all: 2993762 / Scaling rejects: 3
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.901 / Num. unique obs: 22670 / CC1/2: 0.7 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation9.06 Å47.9 Å
Translation9.06 Å47.9 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.3.6data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IS7

3is7


Resolution: 1.45→37.177 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 14.75
RfactorNum. reflection% reflection
Rfree0.1645 22924 5 %
Rwork0.1469 --
obs0.1478 458184 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.69 Å2 / Biso mean: 17.4653 Å2 / Biso min: 6.17 Å2
Refinement stepCycle: final / Resolution: 1.45→37.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15279 0 3 2448 17730
Biso mean--10.72 30.9 -
Num. residues----1872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716149
X-RAY DIFFRACTIONf_angle_d0.87621890
X-RAY DIFFRACTIONf_chiral_restr0.062419
X-RAY DIFFRACTIONf_plane_restr0.0052881
X-RAY DIFFRACTIONf_dihedral_angle_d14.2436194
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.46650.25347790.22911444015219100
1.4665-1.48370.23117990.21671433715136100
1.4837-1.50180.21337360.19721451915255100
1.5018-1.52080.21057580.19071439715155100
1.5208-1.54080.19447960.17841441915215100
1.5408-1.5620.20167870.17621443215219100
1.562-1.58430.19757810.16821442615207100
1.5843-1.60790.19226820.16731448315165100
1.6079-1.6330.18977580.15941446615224100
1.633-1.65980.17877630.15671448615249100
1.6598-1.68840.16227380.1531448315221100
1.6884-1.71910.17367750.1551447015245100
1.7191-1.75220.16787730.14861437715150100
1.7522-1.7880.17817870.14921449515282100
1.788-1.82680.17337470.14631445515202100
1.8268-1.86930.16887760.13941447115247100
1.8693-1.91610.17127530.14431451815271100
1.9161-1.96790.1667940.14281447115265100
1.9679-2.02580.15247180.14051452315241100
2.0258-2.09120.14857740.13491448815262100
2.0912-2.16590.15757620.13331452315285100
2.1659-2.25260.14097560.12591448515241100
2.2526-2.35510.14327920.12761451715309100
2.3551-2.47930.14447510.12641454115292100
2.4793-2.63460.14777570.12831456015317100
2.6346-2.83790.15397960.13891453515331100
2.8379-3.12340.16577550.1472145381529399
3.1234-3.5750.16617830.15441462015403100
3.575-4.50290.14757520.13731470215454100
4.5029-37.18890.17927460.16261508315829100

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