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- PDB-6nlm: 1.90 A resolution structure of WT BfrB from Pseudomonas aeruginos... -

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Basic information

Entry
Database: PDB / ID: 6nlm
Title1.90 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor (analog 15)
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
: / PROTOPORPHYRIN IX CONTAINING FE / Chem-KT1 / Bacterioferritin BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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)234,66351
Polymers222,96212
Non-polymers11,70139
Water23,9961332
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)469,326102
Polymers445,92424
Non-polymers23,40278
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area87240 Å2
ΔGint-206 kcal/mol
Surface area126830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.247, 194.970, 203.030
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
11D-203-

HEM

21D-203-

HEM

31L-202-

HEM

41L-202-

HEM

51L-202-

HEM

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#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

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Non-polymers , 5 types, 1371 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-KT1 / 4-{[3-(4-hydroxy-2-methoxyphenyl)propyl]amino}-1H-isoindole-1,3(2H)-dione


Mass: 326.347 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C18H18N2O4
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1332 / 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: 2.89 Å3/Da / Density % sol: 57.45 % / Mosaicity: 0.16 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 30% (v/v) PEG 200, 0.1M sodium acetate, 0.1M NaCl

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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: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.74 Å / Num. obs: 201747 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.45 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.163 / Net I/σ(I): 9.8 / Num. measured all: 1362877 / Scaling rejects: 2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.154 / Num. measured all: 67675 / Num. unique obs: 9957 / CC1/2: 0.61 / Net I/σ(I) obs: 1.9 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D8O

5d8o


Resolution: 1.9→46.926 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.02 / Phase error: 17.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1837 10141 5.03 %
Rwork0.1518 191506 -
obs0.1534 201647 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.83 Å2 / Biso mean: 20.018 Å2 / Biso min: 8.46 Å2
Refinement stepCycle: final / Resolution: 1.9→46.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15088 0 754 1332 17174
Biso mean--29.72 32.33 -
Num. residues----1863
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 (%)
1.9-1.92160.2843100.243464196729100
1.9216-1.94420.27393440.216962656609100
1.9442-1.96790.24793370.202263526689100
1.9679-1.99280.2213660.191963156681100
1.9928-2.0190.22343330.188563516684100
2.019-2.04670.21883100.177663326642100
2.0467-2.07590.18043460.166463526698100
2.0759-2.10690.22143370.159263196656100
2.1069-2.13990.18533250.148164006725100
2.1399-2.17490.18643400.136563436683100
2.1749-2.21240.18223440.135763626706100
2.2124-2.25270.19193370.139563446681100
2.2527-2.2960.17863340.133163516685100
2.296-2.34290.17633510.130663346685100
2.3429-2.39380.17393420.135163306672100
2.3938-2.44950.17343230.127263786701100
2.4495-2.51070.16953500.125763576707100
2.5107-2.57860.16853200.125863506670100
2.5786-2.65450.16673260.130764136739100
2.6545-2.74020.18073120.136464046716100
2.7402-2.83810.18113650.136163466711100
2.8381-2.95170.17463370.139664066743100
2.9517-3.0860.18083700.151263696739100
3.086-3.24870.18283350.159564036738100
3.2487-3.45220.16783410.149763896730100
3.4522-3.71860.17483470.146963906737100
3.7186-4.09260.16333190.146464706789100
4.0926-4.68440.13683630.130164676830100
4.6844-5.90.19943140.174165376851100
5.9-46.94020.22233630.20156658702199

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