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- PDB-5d8s: 2.55A resolution structure of BfrB (E85A) from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5d8s
Title2.55A resolution structure of BfrB (E85A) from Pseudomonas aeruginosa
ComponentsFerroxidase
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: 2.55 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 17, 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 / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / 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_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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)226,69822
Polymers222,26612
Non-polymers4,43310
Water6,503361
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)453,39744
Polymers444,53124
Non-polymers8,86520
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Buried area65310 Å2
ΔGint-314 kcal/mol
Surface area131130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.556, 205.556, 115.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11I-201-

HEM

21I-201-

HEM

31L-201-

HEM

41L-201-

HEM

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Components

#1: Protein
Ferroxidase /


Mass: 18522.133 Da / Num. of mol.: 12 / Fragment: BfrB / Mutation: E85A
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
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: K
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 15% (v/v) PEG 550MME, 100 mM MES

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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: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→48.98 Å / Num. obs: 80992 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 37.59 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.075 / Net I/σ(I): 10.3 / Num. measured all: 733536 / Scaling rejects: 2
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
2.55-2.69.41.4351.74121444050.620.495100
13.25-48.987.30.04138.248266610.9990.01696.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.93 Å45.28 Å
Translation8.93 Å45.28 Å

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Processing

Software
NameVersionClassification
PHENIXdev_1966refinement
Aimless0.5.2data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IS7

3is7


Resolution: 2.55→42.72 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 3978 4.92 %
Rwork0.1796 --
obs0.1836 80925 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14997 0 304 361 15662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115599
X-RAY DIFFRACTIONf_angle_d1.01821180
X-RAY DIFFRACTIONf_dihedral_angle_d17.2795682
X-RAY DIFFRACTIONf_chiral_restr0.0432325
X-RAY DIFFRACTIONf_plane_restr0.0052714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.58110.35771620.2712694X-RAY DIFFRACTION100
2.5811-2.61380.38961310.2612719X-RAY DIFFRACTION100
2.6138-2.64810.36931420.26442717X-RAY DIFFRACTION100
2.6481-2.68440.35531440.25142688X-RAY DIFFRACTION100
2.6844-2.72280.37231570.24972694X-RAY DIFFRACTION100
2.7228-2.76340.31031480.23592716X-RAY DIFFRACTION100
2.7634-2.80660.31191240.2282725X-RAY DIFFRACTION100
2.8066-2.85260.31471470.20642711X-RAY DIFFRACTION100
2.8526-2.90180.30011460.22282718X-RAY DIFFRACTION100
2.9018-2.95450.34771540.22692701X-RAY DIFFRACTION100
2.9545-3.01130.36541410.24272714X-RAY DIFFRACTION100
3.0113-3.07280.29831250.23442756X-RAY DIFFRACTION100
3.0728-3.13960.30441460.23832712X-RAY DIFFRACTION100
3.1396-3.21260.35971380.21832743X-RAY DIFFRACTION100
3.2126-3.29290.31991310.20922728X-RAY DIFFRACTION100
3.2929-3.38190.25821470.19862731X-RAY DIFFRACTION100
3.3819-3.48130.28021490.18082734X-RAY DIFFRACTION100
3.4813-3.59370.27221340.1752737X-RAY DIFFRACTION100
3.5937-3.7220.25541460.1712742X-RAY DIFFRACTION100
3.722-3.8710.25171340.16172771X-RAY DIFFRACTION100
3.871-4.0470.23831360.15012729X-RAY DIFFRACTION100
4.047-4.26020.22141400.1342763X-RAY DIFFRACTION100
4.2602-4.52680.21341170.12092806X-RAY DIFFRACTION100
4.5268-4.87590.19011540.12762760X-RAY DIFFRACTION100
4.8759-5.36570.16531400.13652794X-RAY DIFFRACTION100
5.3657-6.14020.23121350.16142820X-RAY DIFFRACTION100
6.1402-7.72850.25161540.16612840X-RAY DIFFRACTION100
7.7285-42.72580.17231560.15272984X-RAY DIFFRACTION100

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