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- PDB-3r2h: 1.7 A resolution structure of As-Isolated FtnA from Pseudomonas a... -

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Basic information

Entry
Database: PDB / ID: 3r2h
Title1.7 A resolution structure of As-Isolated FtnA from Pseudomonas aeruginosa (pH 10.5)
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / Bacterial Ferritin / iron binding / iron storage / iron homeostasis / iron release / 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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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)18,2555
Polymers17,9641
Non-polymers2904
Water3,225179
1
A: Bacterioferritin
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)438,111120
Polymers431,14424
Non-polymers6,96796
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 area69360 Å2
ΔGint-329 kcal/mol
Surface area129610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.120, 173.120, 173.120
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-306-

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-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.01 Å3/Da / Density % sol: 59.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 10.5
Details: 20% PEG-8000, 100 mM CAPS, 200 mM NaCl, pH 10.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→29.26 Å / Num. all: 24998 / Num. obs: 24998 / % possible obs: 99.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 41.07 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 27.6232
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.7-1.7936.560.875.21289913528100
1.79-1.942.590.657.61442493387100
1.9-2.0342.60.412.21353813178100
2.03-2.1942.580.25191277353000100
2.19-2.442.410.1826.51175942773100
2.4-2.6942.260.1431.71054372495100
2.69-3.141.840.142.7941412250100
3.1-3.841.20.0758796401933100
3.8-5.3839.90.0678.7609271527100
5.38-29.2635.170.0575.23259992799.48

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.02 Å39.74 Å
Translation2.02 Å39.74 Å

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16data scaling
MOLREPphasing
PHENIXdev_605refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3IS7

3is7


Resolution: 1.7→28.853 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.9279 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 12.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1764 1274 5.1 %RANDOM
Rwork0.1529 ---
obs0.1541 24992 99.98 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.286 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso max: 68.26 Å2 / Biso mean: 14.7357 Å2 / Biso min: 4.09 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 17 179 1455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161331
X-RAY DIFFRACTIONf_angle_d1.3731808
X-RAY DIFFRACTIONf_chiral_restr0.085193
X-RAY DIFFRACTIONf_plane_restr0.007235
X-RAY DIFFRACTIONf_dihedral_angle_d13.428515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7002-1.76830.24021190.198925772696
1.7683-1.84870.22621590.173125572716
1.8487-1.94620.18681510.151825662717
1.9462-2.06810.17161340.147125992733
2.0681-2.22770.15891570.139425822739
2.2277-2.45180.14631530.130626062759
2.4518-2.80630.16221230.145126582781
2.8063-3.53460.18341270.161627102837
3.5346-28.85750.17641510.154828633014

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