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- PDB-3is7: Structure of mineralized Bfrb from Pseudomonas aeruginosa to 2.1A... -

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Basic information

Entry
Database: PDB / ID: 3is7
TitleStructure of mineralized Bfrb from Pseudomonas aeruginosa to 2.1A 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 / MOLREP / Resolution: 2.1 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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)453,55642
Polymers445,92424
Non-polymers7,63218
Water27,2391512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80000 Å2
ΔGint-553 kcal/mol
Surface area131800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.806, 202.756, 207.546
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#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
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1512 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
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 180.00 mm
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.109 / Number: 2179278
ReflectionResolution: 2.1→47.04 Å / Num. obs: 309226 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 16.162
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.007 / Num. unique all: 30544 / Rsym value: 0.669 / % possible all: 99.4
Cell measurementReflection used: 2179278

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0066refinement
PDB_EXTRACT3.005data extraction
d*TREKdata scaling
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLREP
Starting model: PDB entry 1BFR

1bfr


Resolution: 2.1→47.04 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.552 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 15512 5.1 %RANDOM
Rwork0.193 ---
obs0.196 307096 99.85 %-
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: 55.11 Å2 / Biso mean: 27.328 Å2 / Biso min: 12 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2---0.43 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30298 0 522 1512 32332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02131402
X-RAY DIFFRACTIONr_bond_other_d0.0010.0228223
X-RAY DIFFRACTIONr_angle_refined_deg1.8242.01342496
X-RAY DIFFRACTIONr_angle_other_deg0.844365792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.98853675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07125.8551679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.515155972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.24715120
X-RAY DIFFRACTIONr_chiral_restr0.1280.24612
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0234505
X-RAY DIFFRACTIONr_gen_planes_other00.025571
X-RAY DIFFRACTIONr_mcbond_it0.9311.518280
X-RAY DIFFRACTIONr_mcbond_other0.2771.57637
X-RAY DIFFRACTIONr_mcangle_it1.765229305
X-RAY DIFFRACTIONr_scbond_it3.233313122
X-RAY DIFFRACTIONr_scangle_it5.2494.513191
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 (%)
2.1-2.1540.30511450.244212182250899.356
2.154-2.2130.28910800.225208312198399.672
2.213-2.2770.28110200.219203302139099.813
2.277-2.3470.27410450.208197212077999.937
2.347-2.4240.2649800.205191522013999.965
2.424-2.5090.27110390.203184621950699.974
2.509-2.6030.2649610.194178591882499.979
2.603-2.7090.2669400.198171811812899.961
2.709-2.830.2588780.203165341741599.983
2.83-2.9670.2518460.1931581016656100
2.967-3.1270.2647920.201150991589299.994
3.127-3.3160.257700.194142731504699.98
3.316-3.5440.2367090.187133991411599.95
3.544-3.8260.216670.177125691324299.955
3.826-4.1890.196060.155115771218999.951
4.189-4.6790.1865540.141105241108799.919
4.679-5.3950.2245200.1779264978599.99
5.395-6.5890.274280.23279598387100
6.589-9.2380.2273350.1966247658399.985
9.238-500.251970.2383575389796.792

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