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- PDB-6nlg: 1.50 A resolution structure of BfrB (C89S/K96C) from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 6nlg
Title1.50 A resolution structure of BfrB (C89S/K96C) from Pseudomonas aeruginosa in complex with a small molecule fragment (analog 1)
ComponentsBacterioferritin
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
PROTOPORPHYRIN IX CONTAINING FE / : / 5-hydroxy-1H-isoindole-1,3(2H)-dione / Bacterioferritin BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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.ptnr2_symmetry / _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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,06026
Polymers74,1524
Non-polymers3,90722
Water9,854547
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)468,358156
Polymers444,91424
Non-polymers23,444132
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area88870 Å2
ΔGint-1549 kcal/mol
Surface area131750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.814, 153.814, 153.406
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11B-203-

SO4

21B-203-

SO4

31C-202-

HEM

41C-202-

HEM

51D-202-

HEM

61D-202-

HEM

71B-408-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Bacterioferritin


Mass: 18538.066 Da / Num. of mol.: 4 / Mutation: C89S, K96C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bfrB, PA3531 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): ARCTIC EXPRESS RIL / References: UniProt: Q9HY79, ferroxidase

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Non-polymers , 6 types, 569 molecules

#2: Chemical ChemComp-KT7 / 5-hydroxy-1H-isoindole-1,3(2H)-dione


Mass: 163.130 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H5NO3
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.52 Å3/Da / Density % sol: 65.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 35% (v/v) 2-methyl-2,4-pentanediol, 0.1M MES, 0.2M Li2SO4

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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: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→47.84 Å / Num. obs: 168538 / % possible obs: 99.6 % / Redundancy: 19.9 % / Biso Wilson estimate: 17.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.024 / Rrim(I) all: 0.108 / Net I/σ(I): 19.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 20.1 % / Rmerge(I) obs: 1.85 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8167 / CC1/2: 0.768 / Rpim(I) all: 0.417 / Rrim(I) all: 1.897 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.98 Å47.84 Å
Translation6.98 Å47.84 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASER2.5.2phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TOF

4tof


Resolution: 1.5→38.352 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 14.78
RfactorNum. reflection% reflection
Rfree0.1581 8506 5.05 %
Rwork0.1501 --
obs0.1505 168491 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.41 Å2 / Biso mean: 21.0112 Å2 / Biso min: 11.8 Å2
Refinement stepCycle: final / Resolution: 1.5→38.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5087 0 294 547 5928
Biso mean--34.54 33.5 -
Num. residues----624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015614
X-RAY DIFFRACTIONf_angle_d1.0397677
X-RAY DIFFRACTIONf_chiral_restr0.045805
X-RAY DIFFRACTIONf_plane_restr0.006967
X-RAY DIFFRACTIONf_dihedral_angle_d17.6823311
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 (%)
1.5-1.51710.24162810.22595214549599
1.5171-1.53490.23792920.22255204549699
1.5349-1.55360.23133020.21235230553299
1.5536-1.57330.21512940.2095195548999
1.5733-1.5940.23682840.19975222550699
1.594-1.61580.21792580.18535288554699
1.6158-1.63890.17832840.18245241552599
1.6389-1.66340.20322550.17955264551999
1.6634-1.68940.19262780.17725284556299
1.6894-1.71710.18072690.16985270553999
1.7171-1.74670.19482610.16925305556699
1.7467-1.77840.17742840.1585263554799
1.7784-1.81260.17212830.15615295557899
1.8126-1.84960.17192520.1485323557599
1.8496-1.88990.16982730.145153015574100
1.8899-1.93380.1622960.145352805576100
1.9338-1.98220.16183150.138352775592100
1.9822-2.03580.16242660.136953365602100
2.0358-2.09570.14872800.13353405620100
2.0957-2.16330.142850.126453485633100
2.1633-2.24060.13192510.122753775628100
2.2406-2.33030.13282960.121253495645100
2.3303-2.43640.14623060.124853505656100
2.4364-2.56480.13933000.127553645664100
2.5648-2.72540.14562870.134853955682100
2.7254-2.93580.15352960.136654125708100
2.9358-3.23110.13812850.146654335718100
3.2311-3.69830.15373020.142154745776100
3.6983-4.65820.13483290.137655055834100
4.6582-38.3640.18962620.201658466108100

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