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- PDB-3qb9: Mycobacterium tuberculosis bacterioferritin, BfrA -

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Basic information

Entry
Database: PDB / ID: 3qb9
TitleMycobacterium tuberculosis bacterioferritin, BfrA
ComponentsBacterioferritin
KeywordsMETAL BINDING PROTEIN / cytosol / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


Mtb iron assimilation by chelation / response to iron ion / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / iron ion binding / heme binding / extracellular region ...Mtb iron assimilation by chelation / response to iron ion / ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / iron ion binding / heme binding / extracellular region / plasma membrane / 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 / Bacterioferritin BfrA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.11 Å
AuthorsMcMath, L.M. / Goulding, C.W. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Mycobacterium tuberculosis bacterioferritin, BfrA
Authors: McMath, L.M. / Goulding, C.W.
History
DepositionJan 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,99022
Polymers120,4486
Non-polymers2,54316
Water9,170509
1
A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
hetero molecules

A: Bacterioferritin
B: Bacterioferritin
C: Bacterioferritin
D: Bacterioferritin
E: Bacterioferritin
F: Bacterioferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)491,96188
Polymers481,79124
Non-polymers10,17064
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area92330 Å2
ΔGint-527 kcal/mol
Surface area123070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.343, 124.343, 174.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

21A-483-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:159 )
211chain B and (resseq 1:159 )
311chain C and (resseq 1:159 )
411chain D and (resseq 1:159 )
511chain E and (resseq 1:159 )
611chain F and (resseq 1:159 )

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Components

#1: Protein
Bacterioferritin / BFR


Mass: 20074.615 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: bfr, bfrA, MT1925, MTCY180.42c, Rv1876 / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P63697, UniProt: P9WPQ9*PLUS
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.8 M NaCl, 100 mM Tris-HCl (pH 8.0), 25 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.0972109 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2010
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0972109 Å / Relative weight: 1
ReflectionResolution: 2.11→39.321 Å / Num. obs: 75962 / % possible obs: 99.34 % / Redundancy: 9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.303

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.11→39.321 Å / SU ML: 0.62 / σ(F): 1.35 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2363 7640 10.09 %
Rwork0.1783 --
obs0.1842 75688 99.27 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.94 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.373 Å20 Å2-0 Å2
2--3.373 Å2-0 Å2
3----6.7461 Å2
Refinement stepCycle: LAST / Resolution: 2.11→39.321 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7710 0 142 509 8361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077974
X-RAY DIFFRACTIONf_angle_d0.98210824
X-RAY DIFFRACTIONf_dihedral_angle_d14.743030
X-RAY DIFFRACTIONf_chiral_restr0.061200
X-RAY DIFFRACTIONf_plane_restr0.0041416
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1285X-RAY DIFFRACTIONPOSITIONAL
12B1285X-RAY DIFFRACTIONPOSITIONAL0.038
13C1285X-RAY DIFFRACTIONPOSITIONAL0.037
14D1285X-RAY DIFFRACTIONPOSITIONAL0.038
15E1285X-RAY DIFFRACTIONPOSITIONAL0.038
16F1285X-RAY DIFFRACTIONPOSITIONAL0.036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1084-2.13230.38742290.36551984X-RAY DIFFRACTION88
2.1323-2.15740.38532630.33792237X-RAY DIFFRACTION100
2.1574-2.18370.34522320.31372282X-RAY DIFFRACTION100
2.1837-2.21140.30962630.292298X-RAY DIFFRACTION100
2.2114-2.24040.32722470.28242249X-RAY DIFFRACTION99
2.2404-2.27110.32022470.28882268X-RAY DIFFRACTION99
2.2711-2.30360.33852340.25782311X-RAY DIFFRACTION100
2.3036-2.3380.30172640.22932285X-RAY DIFFRACTION100
2.338-2.37450.28622610.2292241X-RAY DIFFRACTION100
2.3745-2.41340.3332430.22142271X-RAY DIFFRACTION100
2.4134-2.4550.27922930.20572235X-RAY DIFFRACTION100
2.455-2.49970.27622740.2172248X-RAY DIFFRACTION100
2.4997-2.54770.28082610.20832295X-RAY DIFFRACTION100
2.5477-2.59970.28432500.212259X-RAY DIFFRACTION100
2.5997-2.65620.28692510.21632290X-RAY DIFFRACTION99
2.6562-2.7180.26672510.20332279X-RAY DIFFRACTION100
2.718-2.7860.2522400.1952306X-RAY DIFFRACTION100
2.786-2.86130.27062470.20172286X-RAY DIFFRACTION100
2.8613-2.94540.25862560.1842286X-RAY DIFFRACTION100
2.9454-3.04050.25782640.18392279X-RAY DIFFRACTION100
3.0405-3.14910.22492410.17112255X-RAY DIFFRACTION100
3.1491-3.27510.24162540.15712308X-RAY DIFFRACTION99
3.2751-3.42410.23682500.14832272X-RAY DIFFRACTION100
3.4241-3.60450.19912320.13612303X-RAY DIFFRACTION100
3.6045-3.83020.17972420.13162290X-RAY DIFFRACTION100
3.8302-4.12560.18462790.12642281X-RAY DIFFRACTION100
4.1256-4.54020.15982550.11382275X-RAY DIFFRACTION100
4.5402-5.19590.19032670.12532305X-RAY DIFFRACTION100
5.1959-6.54140.23012660.17052312X-RAY DIFFRACTION100
6.5414-39.32750.19442840.16642258X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -34.3994 Å / Origin y: -40.8286 Å / Origin z: -1.1453 Å
111213212223313233
T0.1849 Å2-0.053 Å20.0114 Å2-0.2193 Å20.0031 Å2--0.2488 Å2
L0.154 °2-0.0299 °2-0.0853 °2-0.1486 °2-0.0362 °2--0.2993 °2
S0.007 Å °0.0142 Å °0.1038 Å °-0.0282 Å °-0.0103 Å °-0.1007 Å °-0.0715 Å °0.0829 Å °0.002 Å °
Refinement TLS groupSelection details: all

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