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- PDB-5d8y: 2.05A resolution structure of iron bound BfrB (L68A E81A) from Ps... -

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Basic information

Entry
Database: PDB / ID: 5d8y
Title2.05A resolution structure of iron bound BfrB (L68A E81A) from Pseudomonas aeruginosa
ComponentsFerroxidase
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
ACETATE ION / : / 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. / Wang, Y. / Yao, H. / Rivera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1158469 United States
CitationJournal: Biochemistry / Year: 2015
Title: Characterization of the Bacterioferritin/Bacterioferritin Associated Ferredoxin Protein-Protein Interaction in Solution and Determination of Binding Energy Hot Spots.
Authors: Wang, Y. / Yao, H. / Cheng, Y. / Lovell, S. / Battaile, K.P. / Midaugh, C.R. / Rivera, M.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Oct 28, 2015Group: Database references
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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 / 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_atom_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.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: Ferroxidase
B: Ferroxidase
C: Ferroxidase
D: Ferroxidase
E: Ferroxidase
F: Ferroxidase
G: Ferroxidase
H: Ferroxidase
I: Ferroxidase
J: Ferroxidase
K: Ferroxidase
L: Ferroxidase
M: Ferroxidase
N: Ferroxidase
O: Ferroxidase
P: Ferroxidase
Q: Ferroxidase
R: Ferroxidase
S: Ferroxidase
T: Ferroxidase
U: Ferroxidase
V: Ferroxidase
W: Ferroxidase
X: Ferroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,612210
Polymers443,52124
Non-polymers17,091186
Water54,0453000
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area115830 Å2
ΔGint-2346 kcal/mol
Surface area116640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.845, 125.845, 272.518
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX

#1: Protein ...
Ferroxidase


Mass: 18480.053 Da / Num. of mol.: 24 / Fragment: BfrB / Mutation: L68A, E81A
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, 3186 molecules

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


Mass: 55.845 Da / Num. of mol.: 144 / Source method: obtained synthetically / Formula: Fe
#3: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-K / POTASSIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 3000 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% (v/v) 2-methyl-2,4-pentanediol, 100 mM Na acetate, 20 calcium chloride

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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: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→48.75 Å / Num. obs: 302900 / % possible obs: 100 % / Redundancy: 4.9 % / Biso Wilson estimate: 24.44 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.1 / Num. measured all: 1491879
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2% possible all
2.05-2.094.50.7092.167366150040.69299.9
11.23-48.755.60.06234.31011418160.99698.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation9.66 Å48.75 Å
Translation9.66 Å48.75 Å

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IS7

3is7


Resolution: 2.05→48.748 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1963 14740 4.86 %
Rwork0.1509 561893 -
obs0.1531 288073 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.25 Å2 / Biso mean: 27.5792 Å2 / Biso min: 11.19 Å2
Refinement stepCycle: final / Resolution: 2.05→48.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30183 0 762 3000 33945
Biso mean--38.32 36.13 -
Num. residues----3744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131560
X-RAY DIFFRACTIONf_angle_d0.98142807
X-RAY DIFFRACTIONf_chiral_restr0.0464668
X-RAY DIFFRACTIONf_plane_restr0.0065524
X-RAY DIFFRACTIONf_dihedral_angle_d15.24418755
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 (%)
2.05-2.07330.31399030.2732186841958797
2.0733-2.09770.29029770.2482186291960696
2.0977-2.12330.25359080.2278177821869094
2.1233-2.15010.262910060.2211186971970398
2.1501-2.17840.259310340.212189461998098
2.1784-2.20830.253410420.2036189041994698
2.2083-2.23980.24638760.1956187121958898
2.2398-2.27330.22789000.1905188321973298
2.2733-2.30880.234910330.1869185541958798
2.3088-2.34660.23139590.1822188151977497
2.3466-2.38710.23939010.1771186561955797
2.3871-2.43050.2138690.164183931926295
2.4305-2.47720.214210230.1624186971972097
2.4772-2.52780.198911100.1457187981990899
2.5278-2.58280.20489510.1489190181996999
2.5828-2.64280.20879210.1506188441976599
2.6428-2.70890.21098670.1531191792004699
2.7089-2.78220.20279910.1482188911988298
2.7822-2.8640.18568440.1329189091975398
2.864-2.95650.203511410.1456183271946897
2.9565-3.06210.20379870.1403185641955196
3.0621-3.18470.18479430.1397188201976399
3.1847-3.32960.187111180.1411189652008399
3.3296-3.50510.18719350.1328187901972598
3.5051-3.72460.16219670.1254185391950697
3.7246-4.01210.14559630.1158184381940196
4.0121-4.41560.13517840.1023185241930896
4.4156-5.0540.15148410.1124191471998899
5.054-6.36530.194910260.1577189021992899
6.3653-48.76130.19439080.1694189371984598

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