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- PDB-2bk6: The X-ray crystal structure of the Listeria innocua H31G Dps mutant. -

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Basic information

Entry
Database: PDB / ID: 2bk6
TitleThe X-ray crystal structure of the Listeria innocua H31G Dps mutant.
ComponentsNON-HEME IRON-CONTAINING FERRITIN
KeywordsIRON OXIDATION AND STORAGE / DPS (DNA BINDING PROTEIN FROM STARVED CELLS) / FERROXIDASE CENTER / MUTAGENESIS STUDY / METAL TRANSPORT
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA protection during starvation protein
Similarity search - Component
Biological speciesLISTERIA INNOCUA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsIlari, A. / Latella, M.C. / Ribacchi, F. / Su, M. / Giangiacomo, L. / Stefanini, S. / Chasteen, N.D. / Chiancone, E.
Citation
Journal: Biochemistry / Year: 2005
Title: The unusual intersubunit ferroxidase center of Listeria innocua Dps is required for hydrogen peroxide detoxification but not for iron uptake. A study with site-specific mutants.
Authors: Ilari, A. / Latella, M.C. / Ceci, P. / Ribacchi, F. / Su, M. / Giangiacomo, L. / Stefanini, S. / Chasteen, N.D. / Chiancone, E.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: The Dodecameric Ferritin from Listeria Innocua Contains a Novel Intersubunit Iron-Binding Site
Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D.
History
DepositionFeb 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NON-HEME IRON-CONTAINING FERRITIN
B: NON-HEME IRON-CONTAINING FERRITIN
C: NON-HEME IRON-CONTAINING FERRITIN
D: NON-HEME IRON-CONTAINING FERRITIN
E: NON-HEME IRON-CONTAINING FERRITIN
F: NON-HEME IRON-CONTAINING FERRITIN


Theoretical massNumber of molelcules
Total (without water)107,9376
Polymers107,9376
Non-polymers00
Water9,836546
1
A: NON-HEME IRON-CONTAINING FERRITIN
B: NON-HEME IRON-CONTAINING FERRITIN
C: NON-HEME IRON-CONTAINING FERRITIN
D: NON-HEME IRON-CONTAINING FERRITIN
E: NON-HEME IRON-CONTAINING FERRITIN
F: NON-HEME IRON-CONTAINING FERRITIN

A: NON-HEME IRON-CONTAINING FERRITIN
B: NON-HEME IRON-CONTAINING FERRITIN
C: NON-HEME IRON-CONTAINING FERRITIN
D: NON-HEME IRON-CONTAINING FERRITIN
E: NON-HEME IRON-CONTAINING FERRITIN
F: NON-HEME IRON-CONTAINING FERRITIN


Theoretical massNumber of molelcules
Total (without water)215,87412
Polymers215,87412
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_765-x+2,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)136.330, 136.330, 242.489
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 3 / Auth seq-ID: 7 - 156 / Label seq-ID: 7 - 156

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.51371, 0.85797, 0.0005), (0.85795, 0.51369, 0.00634), (0.00518, 0.00368, -0.99998)147.81442, -84.56923, 241.39777
3given(0.42942, -0.24269, -0.86988), (0.75541, -0.43135, 0.49325), (-0.49493, -0.86893, -0.0019)199.73341, -65.25654, 248.10295
4given(0.43034, -0.24168, 0.86971), (0.75786, -0.42667, -0.49356), (0.49036, 0.87152, -0.00045)-11.15555, 53.79253, -5.37477
5given(0.43197, 0.75535, -0.4928), (-0.244, -0.42816, -0.87014), (-0.86826, 0.49612, -0.00065)85.69594, 236.03551, 205.79767
6given(0.42866, 0.75552, 0.49542), (-0.24333, -0.43154, 0.86865), (0.87008, -0.49291, -0.00114)-33.59064, 25.52122, 36.04324

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Components

#1: Protein
NON-HEME IRON-CONTAINING FERRITIN


Mass: 17989.459 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: H31G MUTANT OF DPS FROM LISTERIA INNOCUA / Source: (gene. exp.) LISTERIA INNOCUA (bacteria) / Plasmid: PET-11A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P80725
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A, B, C, D, E, F HIS31GLY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.59 %
Crystal growDetails: PEG 1000 15-30 % W/V, ACETATE BUFFERS IN A PH RANGE BETWEEN 5.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 57503 / % possible obs: 97.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.28 Å / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGH

1qgh


Resolution: 2.19→119.52 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.576 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2883 5 %RANDOM
Rwork0.211 ---
obs0.212 54615 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.39 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.19→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 0 546 7854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227464
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.95710064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5675898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45525.691376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.406151366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5051518
X-RAY DIFFRACTIONr_chiral_restr0.1610.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025618
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1670.24238
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2710.25132
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.2198
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.00524702
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55237213
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.11323220
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.59932851
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 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A600tight positional0.030.05
2B600tight positional0.030.05
3C600tight positional0.030.05
4D600tight positional0.030.05
5E600tight positional0.030.05
6F600tight positional0.030.05
1A607loose positional0.385
2B607loose positional0.375
3C607loose positional0.55
4D607loose positional0.445
5E607loose positional0.335
6F607loose positional0.355
1A600tight thermal0.090.5
2B600tight thermal0.10.5
3C600tight thermal0.120.5
4D600tight thermal0.10.5
5E600tight thermal0.10.5
6F600tight thermal0.10.5
1A607loose thermal1.0610
2B607loose thermal1.0910
3C607loose thermal1.5510
4D607loose thermal1.1310
5E607loose thermal1.0610
6F607loose thermal1.1810
LS refinement shellResolution: 2.19→2.24 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 225
Rwork0.254 3778

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