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- PDB-2wtl: Crystal structure of BfrA from M. tuberculosis -

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Basic information

Entry
Database: PDB / ID: 2wtl
TitleCrystal structure of BfrA from M. tuberculosis
ComponentsBACTERIOFERRITIN
KeywordsMETAL BINDING PROTEIN / BACTERIOFERRITIN A / HEME / IRON / BILIVERDIN / IRON STORAGE / METAL-BINDING
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
: / Unknown ligand / Bacterioferritin / Bacterioferritin BfrA
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsGupta, V. / Gupta, R.K. / Khare, G. / Salunke, D.M. / Tyagi, A.K.
CitationJournal: Plos One / Year: 2009
Title: Crystal Structure of Bfra from Mycobacterium Tuberculosis:Incorporation of Selenomethionine Results in Cleavage and Demetallation of Haem
Authors: Gupta, V. / Gupta, R.K. / Khare, G. / Salunke, D.M. / Tyagi, A.K.
History
DepositionSep 17, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)121,25024
Polymers120,5806
Non-polymers67018
Water3,063170
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)485,00196
Polymers482,32124
Non-polymers2,68172
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area105300 Å2
ΔGint-1051.96 kcal/mol
Surface area122220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.960, 125.960, 175.840
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-1001-

UNX

21A-1002-

UNX

31E-1001-

UNX

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.6885, 0.4623, -0.5589), (0.4627, -0.3134, -0.8293), (-0.5585, -0.8295, 0.001878)-49.48, -73.3, -88.22
2given(0.4634, -0.311, -0.8298), (0.6884, -0.4633, 0.5581), (-0.558, -0.8298, -0.000545)-73.25, 49.37, -88.37
3given(0.3145, 0.4633, 0.8285), (0.4624, 0.6875, -0.5599), (-0.829, 0.5592, 0.00201)73.26, -49.53, -88.23
4given(-0.3737, 0.9276, -2.0E-6), (0.9276, 0.3737, 0.001041), (0.000967, 0.000387, -1)-0.01497, 0.1255, -176.6
5given(0.6856, -0.4644, 0.5605), (-0.4656, 0.3121, 0.8281), (-0.5596, -0.8288, -0.00224)49.47, 73.03, -88.64

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Components

#1: Protein
BACTERIOFERRITIN / BFR


Mass: 20096.705 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: THIS IS A SELENOMETHIONYL ANALOG OF BFRA FROM M. TUBERCULOSIS (RV1876) WITH MSE31, MSE52, MSE107 AND MSE141 INSTEAD OF M31, M52, M107 AND M141
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Description: LABORATORY STRAIN MYCOBACTERIUM TUBERCULOSIS / Plasmid: PET21C-BFRA / 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-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 3 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsUNKNOWN ATOM OR ION (UNX): UNKNOWN ION AT 4-FOLD AXIS PLACED WITH 0.25 OCCUPANCY UNKNOWN (UNL): ...UNKNOWN ATOM OR ION (UNX): UNKNOWN ION AT 4-FOLD AXIS PLACED WITH 0.25 OCCUPANCY UNKNOWN (UNL): POSSIBLE BILIVERDIN REFINED WITH 0.5 OCCUPANCY FE (II) ION ( FE): THESE METAL IONS ARE REFINED WITH LOW OCCUPANCY OF 0.3 AND 0.5

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.8 % / Description: NONE
Crystal growpH: 8
Details: PROTEIN (9MG/ML) WAS CRYSTALLIZED WITH 1.6M NACL; 100MM TRIS-HCL, PH 8.0 AT ROOM TEMPERATURE

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 45901 / % possible obs: 99.4 % / Observed criterion σ(I): 1.6 / Redundancy: 4.4 % / Biso Wilson estimate: 31.49 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.6 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
AUTOMARdata reduction
AUTOMARdata scaling
PHENIXAUTOMR WIZARDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BKN

3bkn


Resolution: 2.59→36.047 Å / SU ML: 1.31 / σ(F): 1.36 / Phase error: 23.01 / Stereochemistry target values: MLHL
Details: FE2 MODELED WITH 0.3 OCCUPANCY RESIDUES 160-162 IN ALL CHAINS MODELED WITH 0.5 OCCUPANCY. UNKNOWN LIGAND (POSSIBLY BLV) MODELED WITH 0.5 OCCUPANCY
RfactorNum. reflection% reflection
Rfree0.2283 1826 4.3 %
Rwork0.183 --
obs0.1849 42380 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.434 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.6935 Å20 Å2-0 Å2
2--0.6935 Å20 Å2
3----1.3869 Å2
Refinement stepCycle: LAST / Resolution: 2.59→36.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7782 0 144 170 8096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168054
X-RAY DIFFRACTIONf_angle_d2.0910922
X-RAY DIFFRACTIONf_dihedral_angle_d18.6763023
X-RAY DIFFRACTIONf_chiral_restr0.0931215
X-RAY DIFFRACTIONf_plane_restr0.011434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.660.28421470.23883128X-RAY DIFFRACTION100
2.66-2.73830.27611440.23663113X-RAY DIFFRACTION100
2.7383-2.82660.29711390.22613112X-RAY DIFFRACTION100
2.8266-2.92760.26521440.22053130X-RAY DIFFRACTION100
2.9276-3.04480.25961340.21453109X-RAY DIFFRACTION100
3.0448-3.18320.25821330.21813111X-RAY DIFFRACTION100
3.1832-3.3510.24191420.2013125X-RAY DIFFRACTION100
3.351-3.56070.22341490.17543132X-RAY DIFFRACTION100
3.5607-3.83540.22281370.15313102X-RAY DIFFRACTION100
3.8354-4.22080.17711440.14523125X-RAY DIFFRACTION100
4.2208-4.83030.16931400.12833150X-RAY DIFFRACTION100
4.8303-6.0810.20311390.17313118X-RAY DIFFRACTION100
6.081-36.05080.22351340.17583099X-RAY DIFFRACTION97

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