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- PDB-4tod: 2.05A resolution structure of BfrB (D34F) from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4tod
Title2.05A resolution structure of BfrB (D34F) from Pseudomonas aeruginosa
ComponentsBacterioferritin
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / iron binding / iron mobilization
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 / : / Bacterioferritin BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsLovell, S. / Battaile, K.P. / Yao, H. / Kumar, R. / Eshelman, K. / Rivera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1158469 United States
CitationJournal: Biochemistry / Year: 2015
Title: Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic.
Authors: Yao, H. / Rui, H. / Kumar, R. / Eshelman, K. / Lovell, S. / Battaile, K.P. / Im, W. / Rivera, M.
History
DepositionJun 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine_hist / 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 / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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.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

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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
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
M: Bacterioferritin
N: Bacterioferritin
O: Bacterioferritin
P: Bacterioferritin
Q: Bacterioferritin
R: Bacterioferritin
S: Bacterioferritin
T: Bacterioferritin
U: Bacterioferritin
V: Bacterioferritin
W: Bacterioferritin
X: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,32742
Polymers446,69424
Non-polymers7,63218
Water37,2192066
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area81750 Å2
ΔGint-617 kcal/mol
Surface area131560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.678, 203.538, 206.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains one biological unit

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Components

#1: Protein ...
Bacterioferritin


Mass: 18612.254 Da / Num. of mol.: 24 / Mutation: D34F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2066 / 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

CrystalColour: Red Prism / Density Matthews: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 35% (v/v) MPD, 0.1M MES, 0.2M Lithium Sulfate

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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: Oct 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→49.41 Å / Num. obs: 328340 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.34 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.048 / Net I/σ(I): 13.1 / Num. measured all: 2240862 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.6 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.05-2.090.9512.2106352160220.710.39798.9
11.23-49.410.02844.11450021980.9990.01298.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
Cootmodel building
XDSdata scaling
PDB_EXTRACT3.14data extraction
MOLREPphasing
PHENIX(phenix.refine: dev_1439)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IS7

3is7


Resolution: 2.05→41.06 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 18.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1921 16559 5.05 %
Rwork0.1533 311642 -
obs0.1552 328201 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.95 Å2 / Biso mean: 28.6421 Å2 / Biso min: 14.01 Å2
Refinement stepCycle: final / Resolution: 2.05→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30343 0 522 2066 32931
Biso mean--25.59 35.67 -
Num. residues----3699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01631471
X-RAY DIFFRACTIONf_angle_d1.26542588
X-RAY DIFFRACTIONf_chiral_restr0.0634612
X-RAY DIFFRACTIONf_plane_restr0.0085449
X-RAY DIFFRACTIONf_dihedral_angle_d16.65711708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.07330.28525270.2339102181074599
2.0733-2.09770.27975430.2165103031084699
2.0977-2.12330.26385540.2014102131076799
2.1233-2.15010.24315530.1867102181077199
2.1501-2.17840.23655340.1762102641079899
2.1784-2.20830.21425160.1667103461086299
2.2083-2.23980.23115510.1648102861083799
2.2398-2.27330.22035200.1635102851080599
2.2733-2.30880.21525360.1549103241086099
2.3088-2.34660.19415260.1523103211084799
2.3466-2.38710.21885580.1561102701082899
2.3871-2.43050.1975560.1502103411089799
2.4305-2.47720.21235610.1519103281088999
2.4772-2.52780.1935400.1455103591089999
2.5278-2.58270.20125340.1464103331086799
2.5827-2.64280.18945790.1472103291090899
2.6428-2.70890.20594870.14991041710904100
2.7089-2.78210.20225510.1536104031095499
2.7821-2.8640.19455870.1491031210899100
2.864-2.95640.20695580.15611042610984100
2.9564-3.0620.20976230.16021033010953100
3.062-3.18460.19935250.16311045210977100
3.1846-3.32940.2015810.16411042811009100
3.3294-3.50490.18625810.15521042211003100
3.5049-3.72430.16825700.14221047611046100
3.7243-4.01170.16515570.14161047311030100
4.0117-4.4150.14455240.11641060111125100
4.415-5.05280.15415730.12851058011153100
5.0528-6.36220.21725680.1771065011218100
6.3622-41.06820.16135860.1542109341152099

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