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- PDB-2bjy: The X-ray crystal structure of Listeria innocua Dps H31G-H43G mutant. -

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Basic information

Entry
Database: PDB / ID: 2bjy
TitleThe X-ray crystal structure of Listeria innocua Dps H31G-H43G mutant.
ComponentsNON-HEME IRON-CONTAINING FERRITIN
KeywordsIRON OXIDATION AND STORAGE / DPS (DNA BINDING PROTEIN FROM STARVED CELLS) / FERROXIDASE CENTER / MUTAGENESIS STUDY / IRON STORAGE / 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: 2.6 Å
AuthorsIlari, A. / Stefanini, S. / 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 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
G: NON-HEME IRON-CONTAINING FERRITIN
H: NON-HEME IRON-CONTAINING FERRITIN
I: NON-HEME IRON-CONTAINING FERRITIN
J: NON-HEME IRON-CONTAINING FERRITIN
K: NON-HEME IRON-CONTAINING FERRITIN
L: NON-HEME IRON-CONTAINING FERRITIN


Theoretical massNumber of molelcules
Total (without water)214,90012
Polymers214,90012
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.625, 132.211, 168.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.54945, -0.69397, 0.46532), (-0.69048, 0.06354, -0.72056), (0.47047, -0.7172, -0.51408)17.56584, 23.05807, 15.85779
3given(-0.52895, 0.65771, 0.53631), (0.66858, -0.06628, 0.74068), (0.5227, 0.75035, -0.40467)15.61592, -21.20887, 12.76921
4given(0.06799, 0.01659, -0.99755), (0.02565, -0.99956, -0.01488), (-0.99736, -0.02457, -0.06839)30.35646, 1.21067, 31.69001
5given(0.9375, -0.21107, 0.27668), (0.1404, -0.49807, -0.8557), (0.31842, 0.84106, -0.4373)-3.05434, 12.36575, 16.4309
6given(-0.23645, -0.85796, 0.45606), (-0.12236, 0.49193, 0.86199), (-0.96391, 0.14802, -0.2213)12.62007, -11.4925, 33.45922
7given(-0.47964, 0.84822, 0.22466), (-0.86196, -0.50338, 0.06027), (0.16421, -0.16474, 0.97257)19.31001, 13.8913, -2.59988
8given(-0.22389, 0.23115, -0.94681), (0.85241, 0.51743, -0.07525), (0.47251, -0.82392, -0.31288)33.9817, -11.91049, 13.43613
9given(0.93665, 0.15375, 0.31471), (-0.20303, -0.49381, 0.84553), (0.28541, -0.85587, -0.43132)-4.12761, -8.93663, 17.96286
10given(-0.47024, -0.868, 0.15954), (0.85239, -0.49354, -0.17279), (0.22873, 0.05474, 0.97195)21.34336, -9.54533, -3.647
11given(-0.21904, 0.84961, 0.47977), (0.22313, 0.5223, -0.82305), (-0.94986, -0.07323, -0.30398)11.00897, 9.46296, 34.89149
12given(-0.24817, -0.13694, -0.95899), (-0.86734, 0.4723, 0.15701), (0.43143, 0.87074, -0.23598)34.61888, 11.8383, 11.35042

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Components

#1: Protein
NON-HEME IRON-CONTAINING FERRITIN / FERRITIN-LIKE PROTEIN


Mass: 17908.363 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: H31G-H43G MUTANT OF DPS FROM LISTERIA INNOCUA / Source: (gene. exp.) LISTERIA INNOCUA (bacteria) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P80725
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: PARTICIPATE IN IRON STORAGE ENGINEERED MUTATION IN CHAIN A, B, C, D, E, F, G, H, I, J, K, ...FUNCTION: PARTICIPATE IN IRON STORAGE ENGINEERED MUTATION IN CHAIN A, B, C, D, E, F, G, H, I, J, K, L HIS 31 TO GLY AND HIS 43 TO GLY

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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: 2.09 Å3/Da / Density % sol: 40.7 %
Crystal growDetails: PEG 1000 15-30% W/V, ACETATE BUFFERS IN A PH RANGE BETWEEN 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 56386 / % possible obs: 93.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.69 Å / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGH

1qgh


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.865 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2820 5 %RANDOM
Rwork0.207 ---
obs0.209 53523 93.7 %-
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14526 0 0 162 14688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02214834
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1571.96119987
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 187
Rwork0.271 3815

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