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- PDB-8ouc: Escherichia coli DPS -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8ouc
TitleEscherichia coli DPS
ComponentsDNA protection during starvation protein
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis / DNA binding ...DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / intracellular iron ion homeostasis / DNA binding / membrane / identical protein binding / cytoplasm
Similarity search - Function
DNA protection during starvation protein, gammaproteobacteria / Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / 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
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsKovalenko, V.V. / Loiko, N.G. / Tereshkina, K.B. / Tereshkin, E.V. / Chulichkov, A.L. / Popov, A.N. / Krupyanskii, Y.F.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation23-24-00250 Russian Federation
CitationJournal: To be published
Title: Escherichia coli DPS
Authors: Kovalenko, V.V. / Loiko, N.G. / Tereshkina, K.B. / Tereshkin, E.V. / Chulichkov, A.L. / Popov, A.N. / Krupyanskii, Y.F.
History
DepositionApr 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Advisory / Database references / Category: citation / pdbx_database_PDB_obs_spr
Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: DNA protection during starvation protein
BBB: DNA protection during starvation protein
CCC: DNA protection during starvation protein
DDD: DNA protection during starvation protein
EEE: DNA protection during starvation protein
FFF: DNA protection during starvation protein
GGG: DNA protection during starvation protein
HHH: DNA protection during starvation protein
III: DNA protection during starvation protein
JJJ: DNA protection during starvation protein
KKK: DNA protection during starvation protein
LLL: DNA protection during starvation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,49919
Polymers224,64412
Non-polymers8557
Water51,4332855
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47780 Å2
ΔGint-98 kcal/mol
Surface area56860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.161, 92.365, 92.391
Angle α, β, γ (deg.)120.117, 98.910, 108.967
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA protection during starvation protein


Mass: 18720.295 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dps, pexB, vtm, b0812, JW0797
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0ABT2, Oxidoreductases; Oxidizing metal ions
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2855 / 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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: TRIS-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.37→80.31 Å / Num. obs: 482862 / % possible obs: 90.4 % / Redundancy: 1.2 % / CC1/2: 0.97 / Net I/σ(I): 8.69
Reflection shellResolution: 1.37→2.03 Å / Num. unique obs: 284282 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→46.121 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.002 / SU ML: 0 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.062
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2061 21618 4.953 %
Rwork0.1872 414841 -
all0.188 --
obs-436459 90.39 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.713 Å2
Baniso -1Baniso -2Baniso -3
1-0.248 Å20.68 Å20.46 Å2
2---0.246 Å20.047 Å2
3----0.385 Å2
Refinement stepCycle: LAST / Resolution: 1.37→46.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14950 0 56 2855 17861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.4060.31115920.30929891X-RAY DIFFRACTION88.1013
1.406-1.4440.32114590.30529336X-RAY DIFFRACTION88.1091
1.444-1.4860.28916050.28428169X-RAY DIFFRACTION88.0549
1.486-1.5320.27614320.26127819X-RAY DIFFRACTION89.1473
1.532-1.5820.27114830.25227217X-RAY DIFFRACTION90.0194
1.582-1.6370.25612650.23226540X-RAY DIFFRACTION90.2145
1.637-1.6990.23913570.21125447X-RAY DIFFRACTION90.149
1.699-1.7680.20613080.19224549X-RAY DIFFRACTION90.16
1.768-1.8470.20412510.18223608X-RAY DIFFRACTION90.3537
1.847-1.9370.20712160.18322321X-RAY DIFFRACTION90.2804
1.937-2.0420.19911800.18921372X-RAY DIFFRACTION90.0819
2.042-2.1660.20310350.18320690X-RAY DIFFRACTION92.1566
2.166-2.3150.1810200.16419597X-RAY DIFFRACTION92.8443
2.315-2.50.1769120.15318275X-RAY DIFFRACTION92.785
2.5-2.7390.1718360.14716641X-RAY DIFFRACTION92.4709
2.739-3.0620.1758700.15214981X-RAY DIFFRACTION92.0446
3.062-3.5340.1536240.14513221X-RAY DIFFRACTION91.4888
3.534-4.3270.1735170.14711395X-RAY DIFFRACTION93.23
4.327-6.110.1994010.1879060X-RAY DIFFRACTION95.5657
6.11-46.1210.2792550.2644715X-RAY DIFFRACTION91.5454

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