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- PDB-3qd8: Crystal structure of Mycobacterium tuberculosis BfrB -

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Basic information

Entry
Database: PDB / ID: 3qd8
TitleCrystal structure of Mycobacterium tuberculosis BfrB
ComponentsProbable bacterioferritin BfrB
KeywordsMETAL BINDING PROTEIN / Ferritin / Iron binding protein / Iron storage
Function / homology
Function and homology information


Mtb iron assimilation by chelation / response to nitrosative stress / encapsulin nanocompartment / iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / peptidoglycan-based cell wall / ferrous iron binding / iron ion transport ...Mtb iron assimilation by chelation / response to nitrosative stress / encapsulin nanocompartment / iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / peptidoglycan-based cell wall / ferrous iron binding / iron ion transport / intracellular iron ion homeostasis / response to hypoxia / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin / 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 ...Ferritin, prokaryotic-type / Ferritin / 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
Ferritin BfrB / Bacterioferritin BfrB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKhare, G. / Gupta, V. / Nangpal, P. / Gupta, R.K. / Sauter, N.K. / Tyagi, A.K.
CitationJournal: Plos One / Year: 2011
Title: Ferritin Structure from Mycobacterium tuberculosis: Comparative Study with Homologues Identifies Extended C-Terminus Involved in Ferroxidase Activity
Authors: Khare, G. / Gupta, V. / Nangpal, P. / Gupta, R.K. / Sauter, N.K. / Tyagi, A.K.
History
DepositionJan 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)491,13424
Polymers491,13424
Non-polymers00
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area72720 Å2
ΔGint-302 kcal/mol
Surface area135500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.068, 226.184, 113.693
Angle α, β, γ (deg.)90.00, 94.44, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T
211U
221V
231W
241X

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 10:164 )A10 - 164
211chain B and (resseq 10:164 )B10 - 164
311chain C and (resseq 10:164 )C10 - 164
411chain D and (resseq 10:164 )D10 - 164
511chain E and (resseq 10:164 )E10 - 164
611chain F and (resseq 10:164 )F10 - 164
711chain G and (resseq 10:164 )G10 - 164
811chain H and (resseq 10:164 )H10 - 164
911chain I and (resseq 10:164 )I10 - 164
1011chain J and (resseq 10:164 )J10 - 164
1111chain K and (resseq 10:164 )K10 - 164
1211chain L and (resseq 10:164 )L10 - 164
1311chain M and (resseq 10:164 )M10 - 164
1411chain N and (resseq 10:164 )N10 - 164
1511chain O and (resseq 10:164 )O10 - 164
1611chain P and (resseq 10:164 )P10 - 164
1711chain Q and (resseq 10:164 )Q10 - 164
1811chain R and (resseq 10:164 )R10 - 164
1911chain S and (resseq 10:164 )S10 - 164
2011chain T and (resseq 10:164 )T10 - 164
2111chain U and (resseq 10:164 )U10 - 164
2211chain V and (resseq 10:164 )V10 - 164
2311chain W and (resseq 10:164 )W10 - 164
2411chain X and (resseq 10:164 )X10 - 164

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Components

#1: Protein ...
Probable bacterioferritin BfrB / Non-heme ferritin Ftn / Nox19


Mass: 20463.936 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: bfrB / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96237, UniProt: P9WNE5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 2.95 Å3/Da / Density % sol: 58.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 3350, 100mM Tris-HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293.15K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 21, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→31.985 Å / Num. obs: 92122 / Redundancy: 2.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.1 / Num. unique all: 13564

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Processing

Software
NameVersionClassificationNB
SCALAdata processing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VLG

1vlg


Resolution: 3→31.985 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8479 / SU ML: 0.48 / σ(F): 1.34 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2361 2008 2.18 %
Rwork0.2099 --
obs0.2105 92083 81.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 9.991 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 117.61 Å2 / Biso mean: 16.3983 Å2 / Biso min: 0.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.5764 Å2-0 Å21.3654 Å2
2---1.0953 Å2-0 Å2
3---2.6718 Å2
Refinement stepCycle: LAST / Resolution: 3→31.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31341 0 0 517 31858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00932178
X-RAY DIFFRACTIONf_angle_d1.05843549
X-RAY DIFFRACTIONf_chiral_restr0.0644808
X-RAY DIFFRACTIONf_plane_restr0.0055889
X-RAY DIFFRACTIONf_dihedral_angle_d18.48611699
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1257X-RAY DIFFRACTIONPOSITIONAL0.043
12B1257X-RAY DIFFRACTIONPOSITIONAL0.043
13C1251X-RAY DIFFRACTIONPOSITIONAL0.053
14D1257X-RAY DIFFRACTIONPOSITIONAL0.046
15E1257X-RAY DIFFRACTIONPOSITIONAL0.051
16F1257X-RAY DIFFRACTIONPOSITIONAL0.05
17G1257X-RAY DIFFRACTIONPOSITIONAL0.052
18H1251X-RAY DIFFRACTIONPOSITIONAL0.05
19I1255X-RAY DIFFRACTIONPOSITIONAL0.063
110J1257X-RAY DIFFRACTIONPOSITIONAL0.05
111K1257X-RAY DIFFRACTIONPOSITIONAL0.051
112L1257X-RAY DIFFRACTIONPOSITIONAL0.053
113M1257X-RAY DIFFRACTIONPOSITIONAL0.044
114N1257X-RAY DIFFRACTIONPOSITIONAL0.051
115O1257X-RAY DIFFRACTIONPOSITIONAL0.052
116P1257X-RAY DIFFRACTIONPOSITIONAL0.052
117Q1257X-RAY DIFFRACTIONPOSITIONAL0.051
118R1257X-RAY DIFFRACTIONPOSITIONAL0.053
119S1257X-RAY DIFFRACTIONPOSITIONAL0.045
120T1257X-RAY DIFFRACTIONPOSITIONAL0.053
121U1257X-RAY DIFFRACTIONPOSITIONAL0.051
122V1257X-RAY DIFFRACTIONPOSITIONAL0.053
123W1257X-RAY DIFFRACTIONPOSITIONAL0.053
124X1257X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.0750.31271470.26546492663982
3.075-3.1580.31821340.24286462659682
3.158-3.25090.25461760.22156460663682
3.2509-3.35570.24611170.22026477659482
3.3557-3.47550.2721500.21046455660581
3.4755-3.61450.18951350.19726334646980
3.6145-3.77870.24141450.18686328647380
3.7787-3.97760.2121350.18046293642880
3.9776-4.22630.16341350.16076291642679
4.2263-4.55180.19871450.16986323646880
4.5518-5.00830.19231500.17086445659581
5.0083-5.72940.24181550.19646633678884
5.7294-7.20480.21981380.21246634677283
7.2048-31.98680.1681460.19126448659480

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