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- PDB-6tb5: The crystal structure of the DPS2 from DEINOCOCCUS RADIODURANS to... -

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Basic information

Entry
Database: PDB / ID: 6tb5
TitleThe crystal structure of the DPS2 from DEINOCOCCUS RADIODURANS to 1.83A resolution (sequentially soaked in CaCl2 [5mM] for 20 min, then in Ammonium iron(II) sulfate [10mM] for 2h).
ComponentsDNA protection during starvation protein 2
KeywordsDNA BINDING PROTEIN / Iron biomineralisation / iron storage / iron detoxification / DNA binding / Calcium binding.
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm
Similarity search - Function
DNA-binding protein Dps / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / DNA protection during starvation protein 2
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsCuypers, M.G. / McSweeney, S. / Romao, C.V. / Mitchell, E.P.
CitationJournal: To Be Published
Title: The crystal structure of the DPS2 from DEINOCOCCUS RADIODURANS to 1.83A resolution (sequentially soaked in CaCl2 [5mM] for 20 min, then in Ammonium iron(II) sulfate [10mM] for 2h).
Authors: Cuypers, M.G. / McSweeney, S. / Romao, C.V. / Mitchell, E.P.
History
DepositionOct 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA protection during starvation protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5937
Polymers23,2901
Non-polymers3046
Water3,099172
1
A: DNA protection during starvation protein 2
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)283,11984
Polymers279,47712
Non-polymers3,64272
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-11
crystal symmetry operation6_544z,-x-1,-y-11
crystal symmetry operation8_454-z-1,x,-y-11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation11_544y,-z-1,-x-11
crystal symmetry operation10_454-y-1,z,-x-11
crystal symmetry operation12_445-y-1,-z-1,x1
crystal symmetry operation7_445-z-1,-x-1,y1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation4_544x,-y-1,-z-11
Unit cell
Length a, b, c (Å)88.830, 88.830, 88.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-304-

FE

21A-305-

FE

31A-451-

HOH

41A-467-

HOH

51A-550-

HOH

61A-551-

HOH

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Components

#1: Protein DNA protection during starvation protein 2


Mass: 23289.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: dps2, dps-2, DR_B0092 / Plasmid: PDEST14 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9RZN1, Oxidoreductases; Oxidizing metal ions
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.52 Å3/Da / Density % sol: 51.1 % / Description: cubes
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M KCl, 0.01M MgCl2, 0.05M HEPES pH 7.0, 5% v/v PEG400 (NATRIX #35)
Temp details: controlled temperature room

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: cryostream frozeon on beamline goniometer
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.83→29.61 Å / Num. obs: 20877 / % possible obs: 99.8 % / Redundancy: 19.6 % / Biso Wilson estimate: 23.3 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.028 / Rrim(I) all: 0.123 / Χ2: 0.98 / Net I/σ(I): 17.2
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 2 / Num. unique obs: 1294 / CC1/2: 0.726 / Rpim(I) all: 0.41 / Χ2: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C6R

2c6r


Resolution: 1.83→28.09 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.63
RfactorNum. reflection% reflection
Rfree0.212 1058 5.07 %
Rwork0.1734 --
obs0.1754 20868 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.61 Å2 / Biso mean: 39.0355 Å2 / Biso min: 17.46 Å2
Refinement stepCycle: final / Resolution: 1.83→28.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1306 0 6 173 1485
Biso mean--46.54 53.43 -
Num. residues----165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.83-1.910.31881090.250424662575100
1.91-2.010.2721250.214224732598100
2.01-2.140.22781500.191524122562100
2.14-2.310.22761280.186124662594100
2.31-2.540.23371350.181224682603100
2.54-2.90.22841220.178324852607100
2.91-3.660.19061490.164124822631100
3.66-28.090.19491400.15652558269899

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