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- PDB-6sev: Structure of Dps from Listeria innocua soaked with 10 mM zinc for... -

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Basic information

Entry
Database: PDB / ID: 6sev
TitleStructure of Dps from Listeria innocua soaked with 10 mM zinc for 120 minutes
ComponentsDNA starvation/stationary phase protection protein
KeywordsMETAL BINDING PROTEIN / Dps / ferritin-like / Iron uptake / iron nucleation / iron storage / biomineralization / zinc
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 starvation/stationary phase protection protein / DNA protection during starvation protein
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZeth, K. / Okuda, M.
CitationJournal: Inorg.Chem. / Year: 2019
Title: Metal Positions and Translocation Pathways of the Dodecameric Ferritin-like Protein Dps.
Authors: Zeth, K. / Sancho-Vaello, E. / Okuda, M.
History
DepositionJul 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA starvation/stationary phase protection protein
B: DNA starvation/stationary phase protection protein
C: DNA starvation/stationary phase protection protein
D: DNA starvation/stationary phase protection protein
E: DNA starvation/stationary phase protection protein
F: DNA starvation/stationary phase protection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,74227
Polymers104,3686
Non-polymers1,37421
Water1,910106
1
A: DNA starvation/stationary phase protection protein
B: DNA starvation/stationary phase protection protein
C: DNA starvation/stationary phase protection protein
D: DNA starvation/stationary phase protection protein
E: DNA starvation/stationary phase protection protein
F: DNA starvation/stationary phase protection protein
hetero molecules

A: DNA starvation/stationary phase protection protein
B: DNA starvation/stationary phase protection protein
C: DNA starvation/stationary phase protection protein
D: DNA starvation/stationary phase protection protein
E: DNA starvation/stationary phase protection protein
F: DNA starvation/stationary phase protection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,48454
Polymers208,73712
Non-polymers2,74742
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area42680 Å2
ΔGint-1787 kcal/mol
Surface area61450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.831, 84.831, 267.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
DNA starvation/stationary phase protection protein


Mass: 17394.734 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: EIB90_09245 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3T1N4C4, UniProt: P80725*PLUS
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 30% PEG1500, 100 mM Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 66812 / % possible obs: 99.7 % / Redundancy: 16.2 % / CC1/2: 0.99 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 2.3 / Num. unique obs: 10607 / CC1/2: 0.33

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→2.02 Å / Cross valid method: THROUGHOUT /
Num. reflection% reflection
obs66806 99.7 %
Refinement stepCycle: LAST / Resolution: 2→2.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7299 0 21 106 7426

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