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- PDB-6nlj: 1.65 A resolution structure of Apo BfrB from Pseudomonas aerugino... -

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Basic information

Entry
Database: PDB / ID: 6nlj
Title1.65 A resolution structure of Apo BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor (analog 12)
ComponentsFerroxidase
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / IRON BINDING / IRON MOBILIZATION / PROTEIN-PROTEIN INTERACTION INHIBITOR
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
: / Chem-KTV / Bacterioferritin BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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)223,88418
Polymers222,96212
Non-polymers9226
Water32,3731797
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)447,76836
Polymers445,92424
Non-polymers1,84412
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area68740 Å2
ΔGint-389 kcal/mol
Surface area130600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.291, 195.014, 203.220
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-244-

HOH

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Components

#1: Protein
Ferroxidase


Mass: 18580.168 Da / Num. of mol.: 12
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: Chemical ChemComp-KTV / 4-{[(3-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione


Mass: 268.267 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H12N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1797 / 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: 2.87 Å3/Da / Density % sol: 57.18 % / Mosaicity: 0.11 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 8% (w/v) PEG 8000, 0.1M 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: Apr 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→47.6 Å / Num. obs: 305152 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 22.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.7 / Num. measured all: 2058004 / Scaling rejects: 2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.131 / Num. unique obs: 15002 / CC1/2: 0.637 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.8data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IS7

3is7


Resolution: 1.65→44.091 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 17.22
RfactorNum. reflection% reflection
Rfree0.1778 15131 4.96 %
Rwork0.1551 --
obs0.1563 305069 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.08 Å2 / Biso mean: 24.7466 Å2 / Biso min: 12.04 Å2
Refinement stepCycle: final / Resolution: 1.65→44.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15129 0 83 1797 17009
Biso mean--36.98 36.95 -
Num. residues----1865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815592
X-RAY DIFFRACTIONf_angle_d0.86921079
X-RAY DIFFRACTIONf_chiral_restr0.0462358
X-RAY DIFFRACTIONf_plane_restr0.0052719
X-RAY DIFFRACTIONf_dihedral_angle_d17.8959427
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.66880.26675020.2394957610078
1.6688-1.68840.27324980.2442957010068
1.6884-1.7090.26685280.2321958510113
1.709-1.73060.25394770.2179960610083
1.7306-1.75340.26054900.211963010120
1.7534-1.77740.23444920.2057965810150
1.7774-1.80280.22684860.195961410100
1.8028-1.82970.23414980.1872962410122
1.8297-1.85830.21865000.1865962110121
1.8583-1.88880.22365060.1916961210118
1.8888-1.92130.19795040.1715962110125
1.9213-1.95630.19145050.1607963810143
1.9563-1.99390.17255230.1513956810091
1.9939-2.03460.17834710.1493963110102
2.0346-2.07880.16334820.1356968910171
2.0788-2.12720.15874960.1381962810124
2.1272-2.18040.16185000.1324963710137
2.1804-2.23930.15924690.127967510144
2.2393-2.30520.15175050.1289967110176
2.3052-2.37960.15985120.1316963510147
2.3796-2.46470.16214990.1332966410163
2.4647-2.56330.15945310.1353965410185
2.5633-2.680.17815020.1393968310185
2.68-2.82130.16915440.1418963710181
2.8213-2.9980.17175150.1455970510220
2.998-3.22940.19555120.1612972410236
3.2294-3.55430.17495580.1522969110249
3.5543-4.06830.16284710.1486981210283
4.0683-5.12430.14245410.1423979510336
5.1243-44.10660.20595140.19681008410598

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