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- PDB-3r2r: 1.65A resolution structure of Iron Soaked FtnA from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 3r2r
Title1.65A resolution structure of Iron Soaked FtnA from Pseudomonas aeruginosa (pH 6.0)
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / iron binding / iron storage / iron homeostasis / iron release / iron mobilization
Function / homology
Function and homology information


iron ion sequestering activity / 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
: / Bacterial ferritin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsLovell, S.W. / Battaile, K.P. / Yao, H. / Jepkorir, G. / Nama, P.V. / Weeratunga, S. / Rivera, M.
CitationJournal: Biochemistry / Year: 2011
Title: Two distinct ferritin-like molecules in Pseudomonas aeruginosa: the product of the bfrA gene is a bacterial ferritin (FtnA) and not a bacterioferritin (Bfr).
Authors: Yao, H. / Jepkorir, G. / Lovell, S. / Nama, P.V. / Weeratunga, S. / Battaile, K.P. / Rivera, M.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Sep 13, 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 / struct_conn / struct_site
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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2516
Polymers17,9641
Non-polymers2875
Water3,207178
1
A: Bacterioferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)438,023144
Polymers431,14424
Non-polymers6,878120
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area70500 Å2
ΔGint-282 kcal/mol
Surface area125010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.729, 170.729, 170.729
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-158-

NA

21A-159-

SO4

31A-159-

SO4

41A-162-

HOH

51A-225-

HOH

61A-259-

HOH

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Components

#1: Protein Bacterioferritin / BFR


Mass: 17964.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: bfr, bfrA, PA4235 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: Q9HWF9
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 35% (v/v) 2-methyl-2,4-pentanediol, 100 mM MES, 200 mM Li2SO4, pH 6.0, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.7401 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7401 Å / Relative weight: 1
ReflectionResolution: 1.65→98.57 Å / Num. all: 25503 / Num. obs: 25503 / % possible obs: 97.26 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 29.22 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 20.8081
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.02 / Num. unique all: 3003 / % possible all: 81.21

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Processing

Software
NameVersionClassificationNB
SCALAdata processing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 3R2H

3r2h


Resolution: 1.65→60.362 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 1293 5.07 %RANDOM
Rwork0.1553 ---
obs0.1567 25491 97.2 %-
all-25491 --
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.916 Å2 / ksol: 0.495 e/Å3
Displacement parametersBiso max: 68.37 Å2 / Biso mean: 16.8556 Å2 / Biso min: 7.29 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→60.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 7 178 1441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141331
X-RAY DIFFRACTIONf_angle_d1.4161807
X-RAY DIFFRACTIONf_chiral_restr0.094196
X-RAY DIFFRACTIONf_plane_restr0.007241
X-RAY DIFFRACTIONf_dihedral_angle_d13.664515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6505-1.71660.27681130.26752024213775
1.7166-1.79470.26571420.197526862828100
1.7947-1.88930.2051580.152527072865100
1.8893-2.00770.16251320.136827292861100
2.0077-2.16270.17481400.133227252865100
2.1627-2.38040.1561650.132427212886100
2.3804-2.72480.18491460.142527692915100
2.7248-3.4330.1691500.147228262976100
3.433-60.40220.18041470.168730113158100

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