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- PDB-2vzb: A Dodecameric Thioferritin in the Bacterial Domain, Characterizat... -

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Basic information

Entry
Database: PDB / ID: 2vzb
TitleA Dodecameric Thioferritin in the Bacterial Domain, Characterization of the Bacterioferritin-Related Protein from Bacteroides fragilis
ComponentsPUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
KeywordsMETAL TRANSPORT / DPS / DPSL / IRON / FERRITIN / OXIDATIVE STRESS
Function / homology
Function and homology information


ferric iron binding / intracellular iron ion homeostasis
Similarity search - Function
DPS-like protein, ferritin-like diiron-binding domain / DNA-binding protein from starved cells-like / 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 ...DPS-like protein, ferritin-like diiron-binding domain / DNA-binding protein from starved cells-like / 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
BENZAMIDINE / : / Putative bacterioferritin-related protein
Similarity search - Component
Biological speciesBACTEROIDES FRAGILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGauss, G.H. / Young, M.J. / Douglas, T. / Lawrence, C.M.
CitationJournal: J.Bacteriol. / Year: 2012
Title: Characterization of the Bacteroides Fragilis Bfr Gene Product Identifies a Bacterial Dps-Like Protein and Suggests Evolutionary Links in the Ferritin Superfamily.
Authors: Gauss, G.H. / Reott, M.A. / Rocha, E.R. / Young, M.J. / Douglas, T. / Smith, C.J. / Lawrence, C.M.
History
DepositionJul 31, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 13, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
B: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
C: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
D: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,08817
Polymers78,4244
Non-polymers66413
Water6,179343
1
A: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
B: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
C: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
D: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
hetero molecules

A: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
B: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
C: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
D: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
hetero molecules

A: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
B: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
C: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
D: PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,26551
Polymers235,27312
Non-polymers1,99239
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
Buried area48200 Å2
ΔGint-622.6 kcal/mol
Surface area67230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.695, 129.695, 129.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 111
2111B1 - 111
3111C1 - 111
4111D1 - 111
1211A120 - 170
2211B120 - 170
3211C120 - 170
4211D120 - 170

NCS oper:
IDCodeMatrixVector
1given(-0.20305, -0.42326, -0.88296), (-0.41975, -0.77706, 0.46903), (-0.88463, 0.46586, -0.01988)26.95959, 113.24398, -29.75611
2given(0.8846, -0.46618, 0.01245), (-0.20909, -0.42036, -0.88294), (0.41684, 0.77845, -0.46932)29.75492, 91.46188, -48.74027
3given(-0.41763, -0.78361, 0.45993), (0.8871, -0.46115, 0.01983), (0.19656, 0.41629, 0.88773)49.13517, 94.23881, -26.32508

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Components

#1: Protein
PUTATIVE BACTERIOFERRITIN-RELATED PROTEIN / BACTERIOFERRITIN-RELATED PROTEIN


Mass: 19606.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES FRAGILIS (bacteria) / Strain: NCTC 9343 / Description: AMERICAN TYPE CULTURE COLLECTION (ATCC) / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LAA6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.34 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M BIS-TRIS HCL PH 8.5, 0.25 M MGCL2, 16 % (W/V) PEG 4,000, 2 % (W/V) BENZAMIDINE HCL, 20 % GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.282
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2.3→37 Å / Num. obs: 34431 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0036refinement
HKL-2000data reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CLB

2clb


Resolution: 2.3→37 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.109 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOLVENT MOLECULES IN THE VICINITY OF X=- 18.9, Y=89.5, Z=10.3 AND X=-1.8, Y=96.5, Z=-5.4 ARE ASSOCIATED WITH RESIDUAL ELECTRON DENSITY A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOLVENT MOLECULES IN THE VICINITY OF X=- 18.9, Y=89.5, Z=10.3 AND X=-1.8, Y=96.5, Z=-5.4 ARE ASSOCIATED WITH RESIDUAL ELECTRON DENSITY A BIS-TRIS BUFFER MOLECULE, USED IN PROTEIN PURIFICATION, MAY OCCUPY EACH OF THESE POSITIONS INSTEAD OF SOME SOLVENT MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1629 5 %RANDOM
Rwork0.195 ---
obs0.197 30759 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5413 0 21 343 5777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225588
X-RAY DIFFRACTIONr_bond_other_d0.0010.023740
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.957564
X-RAY DIFFRACTIONr_angle_other_deg2.523.0029121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6845675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98425.232302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6251530
X-RAY DIFFRACTIONr_chiral_restr0.0630.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026261
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021100
X-RAY DIFFRACTIONr_nbd_refined0.2220.21364
X-RAY DIFFRACTIONr_nbd_other0.2030.23562
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22762
X-RAY DIFFRACTIONr_nbtor_other0.0830.22624
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2312
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.2136
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8421.54435
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84725385
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.52732596
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1554.52176
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2152 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.060.05
2Btight positional0.060.05
3Ctight positional0.060.05
4Dtight positional0.060.05
1Atight thermal0.080.5
2Btight thermal0.080.5
3Ctight thermal0.080.5
4Dtight thermal0.080.5
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.264 121
Rwork0.243 2243

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