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- PDB-3is8: Structure of mineralized Bfrb soaked with FeSO4 from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 3is8
TitleStructure of mineralized Bfrb soaked with FeSO4 from Pseudomonas aeruginosa to 2.25A Resolution
ComponentsBacterioferritin
KeywordsELECTRON TRANSPORT / iron storage / Heme / Iron / Metal-binding
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
: / PROTOPORPHYRIN IX CONTAINING FE / : / Bacterioferritin BfrB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsLovell, S. / Weeratunga, S.K. / Battaile, K.P. / Rivera, M.
CitationJournal: Biochemistry / Year: 2010
Title: Structural Studies of Bacterioferritin B from Pseudomonas aeruginosa Suggest a Gating Mechanism for Iron Uptake via the Ferroxidase Center
Authors: Weeratunga, S.K. / Lovell, S. / Yao, H. / Battaile, K.P. / Fischer, C.J. / Gee, C.E. / Rivera, M.
History
DepositionAug 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.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_alt_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.pdbx_ptnr1_label_alt_id / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
G: Bacterioferritin
H: Bacterioferritin
I: Bacterioferritin
J: Bacterioferritin
K: Bacterioferritin
L: Bacterioferritin
M: Bacterioferritin
N: Bacterioferritin
O: Bacterioferritin
P: Bacterioferritin
Q: Bacterioferritin
R: Bacterioferritin
S: Bacterioferritin
T: Bacterioferritin
U: Bacterioferritin
V: Bacterioferritin
W: Bacterioferritin
X: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,686146
Polymers445,92424
Non-polymers13,762122
Water27,0231500
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.723, 203.278, 207.724
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX

#1: Protein ...
Bacterioferritin


Mass: 18580.168 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bfrB, PA3531 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic express RIL / References: UniProt: Q9HY79

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Non-polymers , 5 types, 1622 molecules

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


Mass: 55.845 Da / Num. of mol.: 96 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1500 / 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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 35% MPD, 100mM MES, 200mM Li2SO4, pH 6.0, vapor diffusion, temperature 277K

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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: Mar 13, 2009
Diffraction measurementDetails: 0.50 degrees, 9.0 sec, detector distance 200.00 mm
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.135 / Number: 1858510
ReflectionResolution: 2.25→50 Å / Num. obs: 251658 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 13.118
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.853 / Num. unique all: 24621 / Rsym value: 0.692 / % possible all: 98.5
Cell measurementReflection used: 1858510

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.36 Å49.36 Å
Translation2.36 Å49.36 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0066refinement
PDB_EXTRACT3.005data extraction
d*TREKdata scaling
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IS7

3is7


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.156 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.196 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 12585 5 %RANDOM
Rwork0.177 ---
obs0.179 250556 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 59.48 Å2 / Biso mean: 24.991 Å2 / Biso min: 4.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30805 0 658 1500 32963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02132037
X-RAY DIFFRACTIONr_bond_other_d00.0228614
X-RAY DIFFRACTIONr_angle_refined_deg1.6832.00843421
X-RAY DIFFRACTIONr_angle_other_deg1.16366847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.04353788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55925.6941728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.963156105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.90815120
X-RAY DIFFRACTIONr_chiral_restr0.1140.24676
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0235252
X-RAY DIFFRACTIONr_gen_planes_other00.025732
X-RAY DIFFRACTIONr_mcbond_it0.8151.518508
X-RAY DIFFRACTIONr_mcbond_other0.2171.57720
X-RAY DIFFRACTIONr_mcangle_it1.626229723
X-RAY DIFFRACTIONr_scbond_it2.838313529
X-RAY DIFFRACTIONr_scangle_it4.6734.513650
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.3080.39270.235171531840898.218
2.308-2.3710.2728950.21169031790199.425
2.371-2.440.2668800.2165051743999.69
2.44-2.5150.2548220.19161161698599.723
2.515-2.5970.2397840.181156411644299.897
2.597-2.6880.2488330.18150611590999.906
2.688-2.7890.2397850.182145931538699.948
2.789-2.9030.2377460.175140351478299.993
2.903-3.0310.2477380.1841349114229100
3.031-3.1790.2216710.1731293213603100
3.179-3.350.2176820.1751227712959100
3.35-3.5520.2095900.1641170912299100
3.552-3.7960.2125690.1581099911568100
3.796-4.0980.1865160.1451025610772100
4.098-4.4860.1625010.12794699970100
4.486-5.0110.1964320.15186319063100
5.011-5.7760.2364220.276038025100
5.776-7.0510.2783470.23365006847100
7.051-9.8740.2052740.16551315405100
9.874-500.2361710.2492966321197.695

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