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- PDB-4to9: 2.0A resolution structure of BfrB (N148L) from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4to9
Title2.0A resolution structure of BfrB (N148L) from Pseudomonas aeruginosa
ComponentsBacterioferritin
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / IRON STORAGE / iron binding / iron mobilization
Function / homology
Function and homology information


ferritin complex / ferroxidase / ferroxidase activity / intracellular sequestering of iron ion / 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 BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
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.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

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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)453,53442
Polymers445,90124
Non-polymers7,63218
Water46,6232588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80190 Å2
ΔGint-612 kcal/mol
Surface area133820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.726, 203.355, 208.266
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: 18579.225 Da / Num. of mol.: 24 / Mutation: N148L
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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2588 / 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: 2.99 Å3/Da / Density % sol: 58.8 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 35% 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: 1.74013 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74013 Å / Relative weight: 1
ReflectionResolution: 2→49.39 Å / Num. obs: 356578 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.11 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.052 / Net I/σ(I): 10.8 / Num. measured all: 2270196
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.034.70.8151.777503165710.6090.40894.1
10.95-49.396.80.04329.71622323960.9970.01798.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
Aimless0.1.29data scaling
PHENIXdev_1450refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IS7

3is7


Resolution: 2→49.39 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 20.85 / Stereochemistry target values: ML / Details: THE FRIEDEL PAIRS WERE USED IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 34746 5.04 %Random
Rwork0.1691 654121 --
obs0.1712 688867 98.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.52 Å2 / Biso mean: 26.0157 Å2 / Biso min: 10.28 Å2
Refinement stepCycle: final / Resolution: 2→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30466 0 1038 2588 34092
Biso mean--28.04 32.89 -
Num. residues----3712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132170
X-RAY DIFFRACTIONf_angle_d0.97543674
X-RAY DIFFRACTIONf_chiral_restr0.0434648
X-RAY DIFFRACTIONf_plane_restr0.0065512
X-RAY DIFFRACTIONf_dihedral_angle_d17.3111946
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 (%)
2-2.02270.342610190.3061196922071189
2.0227-2.04650.326711020.2827215222262497
2.0465-2.07150.315911640.2641218702303499
2.0715-2.09770.278612090.2472203523244100
2.0977-2.12530.272411650.2241218912305699
2.1253-2.15440.255311410.213219362307799
2.1544-2.18520.256911000.2075220132311399
2.1852-2.21780.256411440.1959219002304499
2.2178-2.25250.225911090.1867219392304899
2.2525-2.28940.24912270.18292190123128100
2.2894-2.32890.240810780.17852205423132100
2.3289-2.37120.227812410.17612191523156100
2.3712-2.41680.211912040.16222195023154100
2.4168-2.46620.220211850.1641218792306499
2.4662-2.51980.214811340.1567219662310099
2.5198-2.57840.22411880.162216892287799
2.5784-2.64290.214410890.15772202323112100
2.6429-2.71430.212712110.15882194223153100
2.7143-2.79420.224510810.16892204923130100
2.7942-2.88440.21211300.1595219462307699
2.8844-2.98750.221611360.1661219092304599
2.9875-3.1070.226811930.1723218312302499
3.107-3.24840.223612050.1811217182292399
3.2484-3.41970.206112250.1703218392306499
3.4197-3.63380.194912030.157218012300499
3.6338-3.91430.191711950.1553217252292099
3.9143-4.3080.154112170.1262215462276398
4.308-4.93090.143711400.1256218312297199
4.9309-6.21050.199111820.1692219422312499
6.2105-49.40360.176511290.1605218672299699

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