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- PDB-6gcm: Escherichia coli DPS -

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Basic information

Entry
Database: PDB / ID: 6gcm
TitleEscherichia coli DPS
Components(DNA protection during starvation protein) x 4
KeywordsDNA BINDING PROTEIN / DNA-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 / identical protein binding / membrane / 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, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like ...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, 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKovalenko, V.V. / Loiko, N.G. / Tereshkin, E.V. / Tereshkina, K.B. / Chulichkov, A.L. / Popov, A.N. / Krupyanskii, Y.F.
Funding support2items
OrganizationGrant numberCountry
Russian Ministry of Education and Science14.616.21.0070
Federal agency of scientific organizationsAAAA-A17-117040610310-6
CitationJournal: To Be Published
Title: Escherichia coli DPS
Authors: Kovalenko, V.V. / Loiko, N.G. / Tereshkin, E.V. / Tereshkina, K.B. / Chulichkov, A.L. / Popov, A.N. / Krupyanskii, Y.F.
History
DepositionApr 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
G: DNA protection during starvation protein
H: DNA protection during starvation protein
I: DNA protection during starvation protein
J: DNA protection during starvation protein
K: DNA protection during starvation protein
L: DNA protection during starvation protein
b: DNA protection during starvation protein
c: DNA protection during starvation protein
d: DNA protection during starvation protein
e: DNA protection during starvation protein
f: DNA protection during starvation protein
g: DNA protection during starvation protein
h: DNA protection during starvation protein
i: DNA protection during starvation protein
j: DNA protection during starvation protein
k: DNA protection during starvation protein
l: DNA protection during starvation protein
m: DNA protection during starvation protein


Theoretical massNumber of molelcules
Total (without water)417,60524
Polymers417,60524
Non-polymers00
Water17,186954
1
A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein
D: DNA protection during starvation protein
E: DNA protection during starvation protein
F: DNA protection during starvation protein
G: DNA protection during starvation protein
H: DNA protection during starvation protein
I: DNA protection during starvation protein
J: DNA protection during starvation protein
K: DNA protection during starvation protein
L: DNA protection during starvation protein


Theoretical massNumber of molelcules
Total (without water)208,99712
Polymers208,99712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44800 Å2
ΔGint-137 kcal/mol
Surface area56450 Å2
MethodPISA
2
b: DNA protection during starvation protein
c: DNA protection during starvation protein
d: DNA protection during starvation protein
e: DNA protection during starvation protein
f: DNA protection during starvation protein
g: DNA protection during starvation protein
h: DNA protection during starvation protein
i: DNA protection during starvation protein
j: DNA protection during starvation protein
k: DNA protection during starvation protein
l: DNA protection during starvation protein
m: DNA protection during starvation protein


Theoretical massNumber of molelcules
Total (without water)208,60812
Polymers208,60812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44820 Å2
ΔGint-143 kcal/mol
Surface area56280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.150, 89.420, 150.650
Angle α, β, γ (deg.)90.00, 90.24, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein DNA protection during starvation protein


Mass: 17859.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12
References: UniProt: P0ABT2, Oxidoreductases; Oxidizing metal ions
#2: Protein
DNA protection during starvation protein


Mass: 17356.645 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12
References: UniProt: P0ABT2, Oxidoreductases; Oxidizing metal ions
#3: Protein DNA protection during starvation protein


Mass: 17571.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dps, pexB, vtm, b0812, JW0797 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P0ABT2, Oxidoreductases; Oxidizing metal ions
#4: Protein DNA protection during starvation protein


Mass: 16967.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (strain K12) (bacteria) / Strain: K12
References: UniProt: P0ABT2, Oxidoreductases; Oxidizing metal ions
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 954 / Source method: isolated from a natural source / Formula: H2O

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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: 49.21 %
Crystal growTemperature: 291 K / Method: evaporation, recrystallization / Details: PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 2.45→150.65 Å / Num. obs: 138619 / % possible obs: 99.23 % / Redundancy: 1 % / Net I/σ(I): 8.11
Reflection shellResolution: 2.45→2.514 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DPS

1dps


Resolution: 2.45→100.02 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.887 / SU B: 13.292 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.649 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25805 7407 5 %RANDOM
Rwork0.20273 ---
obs0.20547 139323 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.105 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0 Å2-0.73 Å2
2---0.29 Å2-0 Å2
3---1.43 Å2
Refinement stepCycle: 1 / Resolution: 2.45→100.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29282 0 0 954 30236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01929711
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.94940286
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48853679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03924.9321466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.455155292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1515192
X-RAY DIFFRACTIONr_chiral_restr0.1150.24760
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222232
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_it2.1063.52714788
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2895.28118443
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9123.68214923
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.03815.8946663
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: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 534 -
Rwork0.377 10263 -
obs--99.44 %

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