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- PDB-3r2s: 2.1A resolution structure of Doubly Soaked FtnA from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3r2s
Title2.1A resolution structure of Doubly 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: 2.1 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)18,3077
Polymers17,9641
Non-polymers3426
Water1,15364
1
A: Bacterioferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)439,363168
Polymers431,14424
Non-polymers8,218144
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 area68080 Å2
ΔGint-322 kcal/mol
Surface area127390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.162, 171.162, 171.162
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-159-

NA

21A-160-

SO4

31A-160-

SO4

41A-182-

HOH

51A-223-

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.: 4 / 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.: 64 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
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: 2.1→98.82 Å / Num. all: 13093 / Num. obs: 13093 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 37.18 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 32.9568
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.1-2.2137.850.765.89699911849100
2.21-2.3536.640.489.27647771768100
2.35-2.5138.010.3114.02629471656100
2.51-2.7137.830.2119.9589741559100
2.71-2.9737.090.1232.04533751439100
2.97-3.3239.10.0844.92513041312100
3.32-3.8336.490.0661.31428011173100
3.83-4.736.940.0576.12375691017100
4.7-6.6435.370.0569.2628686811100
6.64-98.8232.240.0477.471641050999.85

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data processing
PHENIX1.7_634refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3R2H

3r2h


Resolution: 2.1→51.607 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 641 4.9 %RANDOM
Rwork0.1942 ---
obs0.1969 13092 100 %-
all-13092 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.564 Å2 / ksol: 0.483 e/Å3
Displacement parametersBiso max: 80.27 Å2 / Biso mean: 38.268 Å2 / Biso min: 20.36 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→51.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 8 64 1331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161299
X-RAY DIFFRACTIONf_angle_d1.461754
X-RAY DIFFRACTIONf_chiral_restr0.091190
X-RAY DIFFRACTIONf_plane_restr0.008232
X-RAY DIFFRACTIONf_dihedral_angle_d15.299496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.26220.27421250.215824032528
2.2622-2.48980.32951340.206324212555
2.4898-2.85010.26561110.200624702581
2.8501-3.59070.28411280.18924922620
3.5907-51.62280.20991430.189226652808

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