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- PDB-4toh: 1.80A resolution structure of Iron Bound BfrB (C89S, K96C) from P... -

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Basic information

Entry
Database: PDB / ID: 4toh
Title1.80A resolution structure of Iron Bound BfrB (C89S, K96C) from Pseudomonas aeruginosa
ComponentsBacterioferritin
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / iron binding / iron mobilization
Function / homology
Function and homology information


ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / 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
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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: Advisory / Author supporting evidence ...Advisory / 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 / pdbx_validate_symm_contact / 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 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / 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 / 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.ptnr1_symmetry / _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_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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.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: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,29947
Polymers74,1524
Non-polymers4,14743
Water13,475748
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)469,795282
Polymers444,91424
Non-polymers24,882258
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 area127740 Å2
ΔGint-3133 kcal/mol
Surface area123370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.993, 153.993, 155.200
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-211-

SO4

21B-211-

SO4

31C-201-

HEM

41C-201-

HEM

51D-201-

HEM

61D-201-

HEM

71A-319-

HOH

DetailsThe biological unit (24-mer) can be generated by applying the following symmetry operators on the asymmetric unit: X, X-Y-1, -Z-1/2 -X+Y, Y, -Z-1/2 -X+Y, -X-1, Z -Y-1, X-Y-1, Z -Y-1, -X-1, -Z-1/2

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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) / 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, 791 molecules

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


Mass: 55.845 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 748 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsB211 LIES ON A 3-FOLDS AXIS, THE S AND O3 ATOMS ARE GENERATED BY THE SYMMETRY OPERATION

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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: 3.58 Å3/Da / Density % sol: 65.66 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
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: 1.73963 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73963 Å / Relative weight: 1
ReflectionRedundancy: 17.2 % / Number: 1260361 / Rmerge(I) obs: 0.119 / D res high: 2 Å / D res low: 48.25 Å / Num. obs: 73277 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
22.0411.0827.1
9.848.2510.06417
ReflectionResolution: 1.8→48.23 Å / Num. obs: 99837 / % possible obs: 99.7 % / Redundancy: 18.3 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.028 / Net I/σ(I): 22.3 / Num. measured all: 1825740
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.8-1.8310.21.3131.84801047210.7010.42796.5
9.86-48.2317.30.07765.4128037390.9970.01899.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.2.8data scaling
XDSdata scaling
PHASERphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: dev_1701)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IS7

3is7


Resolution: 1.8→48.23 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 16.99 / Stereochemistry target values: ML / Details: THE FRIEDEL PAIRS WERE USED IN REFINEMENT
RfactorNum. reflection% reflection
Rfree0.1717 9520 5.01 %
Rwork0.1473 180676 -
obs0.1485 99803 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.51 Å2 / Biso mean: 24.8208 Å2 / Biso min: 10.1 Å2
Refinement stepCycle: final / Resolution: 1.8→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5078 0 218 748 6044
Biso mean--30.58 35.43 -
Num. residues----624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095476
X-RAY DIFFRACTIONf_angle_d1.0137461
X-RAY DIFFRACTIONf_chiral_restr0.044792
X-RAY DIFFRACTIONf_plane_restr0.006954
X-RAY DIFFRACTIONf_dihedral_angle_d16.8552043
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 (%)
1.8-1.82050.31983440.29465773611796
1.8205-1.84190.29433040.26895916622097
1.8419-1.86430.26763260.24255931625798
1.8643-1.88790.25913070.22525975628299
1.8879-1.91280.22862720.208160726344100
1.9128-1.9390.2143310.199160176348100
1.939-1.96670.21672910.182260406331100
1.9667-1.9960.21313350.178560426377100
1.996-2.02720.20032740.178160726346100
2.0272-2.06050.19113130.164260256338100
2.0605-2.0960.21393000.15960426342100
2.096-2.13410.18413130.155560596372100
2.1341-2.17520.16983060.14660296335100
2.1752-2.21960.17743000.136760586358100
2.2196-2.26780.17743360.129960496385100
2.2678-2.32060.15233310.129560236354100
2.3206-2.37860.1662950.13660896384100
2.3786-2.44290.16563290.135360056334100
2.4429-2.51480.15513390.127160466385100
2.5148-2.5960.14763050.130860546359100
2.596-2.68870.16133670.129659816348100
2.6887-2.79640.16623570.132860126369100
2.7964-2.92360.16872880.13460556343100
2.9236-3.07770.16793010.136560836384100
3.0777-3.27050.14032820.140760806362100
3.2705-3.5230.17423730.137459756348100
3.523-3.87740.1512970.135960626359100
3.8774-4.43810.12433330.112660326365100
4.4381-5.59020.15213300.141860486378100
5.5902-48.24880.20063410.173860316372100

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