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- PDB-6tgt: The Calcium soaked crystal structure of the DPS2 from DEINOCOCCUS... -

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Basic information

Entry
Database: PDB / ID: 6tgt
TitleThe Calcium soaked crystal structure of the DPS2 from DEINOCOCCUS RADIODURANS to 2.16A resolution (Soaked in CaCl2 [5mM] for 20 min).
ComponentsDNA protection during starvation protein 2
KeywordsDNA BINDING PROTEIN / Iron biomineralisation / iron storage / iron detoxification / DNA binding / Calcium binding / metalloprotein.
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: 2.155 Å
AuthorsCuypers, M.G. / Romao, C.V. / Mitchell, E.P. / McSweeney, S.
CitationJournal: To Be Published
Title: The Calcium soaked crystal structure of the DPS2 from DEINOCOCCUS RADIODURANS to 2.16A resolution (Soaked in CaCl2 [5mM] for 20 min).
Authors: Cuypers, M.G. / McSweeney, S. / Romao, C.V. / Mitchell, E.P.
History
DepositionNov 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 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)23,2525
Polymers23,0751
Non-polymers1764
Water2,072115
1
A: DNA protection during starvation protein 2
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)279,01960
Polymers276,90612
Non-polymers2,11348
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
Buried area55290 Å2
ΔGint-1189 kcal/mol
Surface area51790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.342, 88.342, 88.342
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-303-

CA

21A-304-

CA

31A-434-

HOH

41A-463-

HOH

51A-510-

HOH

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Components

#1: Protein DNA protection during starvation protein 2


Mass: 23075.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: dps2, dps-2, DR_B0092 / Plasmid: PDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: Q9RZN1, Oxidoreductases; Oxidizing metal ions
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.47 Å3/Da / Density % sol: 50.3 % / Description: cube
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M KCl, 0.01 M MgCl2, 0.05 M HEPES pH 7.0, 5% v/v PEG 400 (Hampton Natrix crystal screen # 35)
Temp details: regulated temperature room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream N2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.155→51 Å / Num. obs: 12682 / % possible obs: 100 % / Redundancy: 10.6 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.041 / Rrim(I) all: 0.133 / Χ2: 0.92 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.155-2.2210.71.441210590.7210.4791.581.18100
8.89-517.90.04263.82090.9950.0170.0451.6899

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c2j

2c2j


Resolution: 2.155→44.21 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.177
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 587 4.6 %RANDOM
Rwork0.207 ---
obs0.2084 12087 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.16 Å2 / Biso mean: 36.114 Å2 / Biso min: 17.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.155→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 4 117 1406
Biso mean--48.71 44.27 -
Num. residues----163
LS refinement shellResolution: 2.157→2.213 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.38 44 -
Rwork0.343 867 -
obs--100 %

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