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- PDB-3oj5: Mycobacterium tuberculosis ferritin homolog, BfrB -

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Basic information

Entry
Database: PDB / ID: 3oj5
TitleMycobacterium tuberculosis ferritin homolog, BfrB
ComponentsFerritin family protein
KeywordsOXIDOREDUCTASE / ferroxidase / cytosol
Function / homology
Function and homology information


ferric iron binding / iron ion transport / intracellular iron ion homeostasis
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Ferritin, prokaryotic-type / Ferritin, core subunit, four-helix bundle / Ferritin / 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 speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.845 Å
AuthorsMcMath, L.M. / Goulding, C.W.
CitationJournal: To be Published
Title: Mycobacterium tuberculosis ferritin homolog, BfrB
Authors: McMath, L.M. / Goulding, C.W.
History
DepositionAug 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)514,48724
Polymers514,48724
Non-polymers00
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area67480 Å2
ΔGint-202 kcal/mol
Surface area139070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.768, 231.997, 114.324
Angle α, β, γ (deg.)90.00, 94.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11O-195-

HOH

21S-207-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 9:164 )
211CHAIN B AND (RESSEQ 9:164 )
311CHAIN C AND (RESSEQ 9:164 )
411CHAIN D AND (RESSEQ 9:164 )
511CHAIN E AND (RESSEQ 9:164 )
611CHAIN F AND (RESSEQ 9:164 )
711CHAIN G AND (RESSEQ 9:164 )
811CHAIN H AND (RESSEQ 9:164 )
911CHAIN I AND (RESSEQ 9:164 )
1011CHAIN J AND (RESSEQ 9:164 )
1111CHAIN K AND (RESSEQ 9:164 )
1211CHAIN L AND (RESSEQ 9:164 )
1311CHAIN M AND (RESSEQ 9:164 )
1411CHAIN N AND (RESSEQ 9:164 )
1511CHAIN O AND (RESSEQ 9:164 )
1611CHAIN P AND (RESSEQ 9:164 )
1711CHAIN Q AND (RESSEQ 9:164 )
1811CHAIN R AND (RESSEQ 9:164 )
1911CHAIN S AND (RESSEQ 9:164 )
2011CHAIN T AND (RESSEQ 9:164 )
2111CHAIN U AND (RESSEQ 9:164 )
2211CHAIN V AND (RESSEQ 9:164 )
2311CHAIN W AND (RESSEQ 9:164 )
2411CHAIN X AND (RESSEQ 9:164 )

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Components

#1: Protein ...
Ferritin family protein


Mass: 21436.947 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25177 / H37Ra / Gene: bfrB, MRA_3881, Rv3841 / Plasmid: pET28b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A5U9H0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 58.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 14% (w/v) PEG 3350, 5% (w/v) Tacsimate, 100 mM glycine, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2009
Details: vertically collimating premirror, LN2 cooled double-crystal silicon (111) monoc hromator, toroidal focusing M2 mirror
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.845→49.899 Å / Num. obs: 139618 / % possible obs: 98.94 % / Redundancy: 4.7 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.845→49.899 Å / SU ML: 0.81 / σ(F): 1.35 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 6983 5.02 %
Rwork0.2075 --
obs0.2091 139070 98.93 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.086 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.5115 Å2-0 Å21.4216 Å2
2---9.37 Å20 Å2
3---14.8815 Å2
Refinement stepCycle: LAST / Resolution: 2.845→49.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30624 0 0 330 30954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01531176
X-RAY DIFFRACTIONf_angle_d1.19842168
X-RAY DIFFRACTIONf_dihedral_angle_d17.19711544
X-RAY DIFFRACTIONf_chiral_restr0.084680
X-RAY DIFFRACTIONf_plane_restr0.0055664
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1268X-RAY DIFFRACTIONPOSITIONAL
12B1268X-RAY DIFFRACTIONPOSITIONAL0.112
13C1268X-RAY DIFFRACTIONPOSITIONAL0.11
14D1268X-RAY DIFFRACTIONPOSITIONAL0.143
15E1268X-RAY DIFFRACTIONPOSITIONAL0.144
16F1268X-RAY DIFFRACTIONPOSITIONAL0.138
17G1268X-RAY DIFFRACTIONPOSITIONAL0.104
18H1268X-RAY DIFFRACTIONPOSITIONAL0.111
19I1268X-RAY DIFFRACTIONPOSITIONAL0.09
110J1268X-RAY DIFFRACTIONPOSITIONAL0.114
111K1268X-RAY DIFFRACTIONPOSITIONAL0.149
112L1268X-RAY DIFFRACTIONPOSITIONAL0.116
113M1268X-RAY DIFFRACTIONPOSITIONAL0.123
114N1268X-RAY DIFFRACTIONPOSITIONAL0.113
115O1268X-RAY DIFFRACTIONPOSITIONAL0.094
116P1268X-RAY DIFFRACTIONPOSITIONAL0.114
117Q1268X-RAY DIFFRACTIONPOSITIONAL0.121
118R1268X-RAY DIFFRACTIONPOSITIONAL0.12
119S1268X-RAY DIFFRACTIONPOSITIONAL0.09
120T1268X-RAY DIFFRACTIONPOSITIONAL0.115
121U1268X-RAY DIFFRACTIONPOSITIONAL0.11
122V1268X-RAY DIFFRACTIONPOSITIONAL0.115
123W1268X-RAY DIFFRACTIONPOSITIONAL0.109
124X1268X-RAY DIFFRACTIONPOSITIONAL0.113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.845-2.87750.35651820.30993485X-RAY DIFFRACTION78
2.8775-2.91140.3452290.30344434X-RAY DIFFRACTION99
2.9114-2.94690.32562530.27634400X-RAY DIFFRACTION100
2.9469-2.98420.3112260.24714400X-RAY DIFFRACTION99
2.9842-3.02340.28052160.2384417X-RAY DIFFRACTION99
3.0234-3.06480.29872330.23394412X-RAY DIFFRACTION100
3.0648-3.10860.26982120.22014465X-RAY DIFFRACTION100
3.1086-3.1550.29142340.23134433X-RAY DIFFRACTION100
3.155-3.20430.27212220.22464400X-RAY DIFFRACTION100
3.2043-3.25680.26952250.21034468X-RAY DIFFRACTION100
3.2568-3.3130.2722660.2144367X-RAY DIFFRACTION100
3.313-3.37320.26322130.22174446X-RAY DIFFRACTION100
3.3732-3.43810.27092390.21924402X-RAY DIFFRACTION100
3.4381-3.50820.24252340.21294446X-RAY DIFFRACTION100
3.5082-3.58450.20332300.19364425X-RAY DIFFRACTION100
3.5845-3.66780.24732540.20744425X-RAY DIFFRACTION100
3.6678-3.75950.25422400.20424406X-RAY DIFFRACTION100
3.7595-3.86110.25362440.20734430X-RAY DIFFRACTION100
3.8611-3.97470.23012140.20494455X-RAY DIFFRACTION100
3.9747-4.10290.1982630.1674437X-RAY DIFFRACTION100
4.1029-4.24950.16512340.15364426X-RAY DIFFRACTION100
4.2495-4.41960.17692310.15474459X-RAY DIFFRACTION100
4.4196-4.62060.1912320.16774425X-RAY DIFFRACTION100
4.6206-4.8640.2232440.19174456X-RAY DIFFRACTION100
4.864-5.16840.19652410.16884459X-RAY DIFFRACTION100
5.1684-5.5670.23952380.21484436X-RAY DIFFRACTION100
5.567-6.12630.28892210.25114480X-RAY DIFFRACTION100
6.1263-7.01080.23262510.21694459X-RAY DIFFRACTION100
7.0108-8.82480.1942250.18354503X-RAY DIFFRACTION100
8.8248-49.90660.23022370.23914431X-RAY DIFFRACTION98

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