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- PDB-8pw0: Manganese-dependent transcriptional repressor DR2539 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 8pw0
TitleManganese-dependent transcriptional repressor DR2539 complexed with manganese and bound to dr1709 promotor
Components
  • DNA (5'-D(*TP*AP*TP*TP*TP*TP*AP*GP*GP*CP*GP*CP*GP*AP*CP*TP*AP*AP*AP*AP*T)-3')
  • Iron dependent repressor, putative
KeywordsDNA BINDING PROTEIN / Transcriptional regulator
Function / homology
Function and homology information


transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
FeoA domain / Ferrous iron transporter FeoA domain / FeoA / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain ...FeoA domain / Ferrous iron transporter FeoA domain / FeoA / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Manganese transport regulator
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMota, C. / De Sanctis, D.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaSFRH/BEST/51724/2011 Portugal
Fundacao para a Ciencia e a Tecnologia35797UH Portugal
CitationJournal: Febs J. / Year: 2024
Title: Metal ion activation and DNA recognition by the Deinococcus radiodurans manganese sensor DR2539.
Authors: Mota, C. / Webster, M. / Saidi, M. / Kapp, U. / Zubieta, C. / Giachin, G. / Manso, J.A. / de Sanctis, D.
History
DepositionJul 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron dependent repressor, putative
B: DNA (5'-D(*TP*AP*TP*TP*TP*TP*AP*GP*GP*CP*GP*CP*GP*AP*CP*TP*AP*AP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6957
Polymers22,3832
Non-polymers3125
Water1,65792
1
A: Iron dependent repressor, putative
B: DNA (5'-D(*TP*AP*TP*TP*TP*TP*AP*GP*GP*CP*GP*CP*GP*AP*CP*TP*AP*AP*AP*AP*T)-3')
hetero molecules

A: Iron dependent repressor, putative
B: DNA (5'-D(*TP*AP*TP*TP*TP*TP*AP*GP*GP*CP*GP*CP*GP*AP*CP*TP*AP*AP*AP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,39014
Polymers44,7664
Non-polymers62410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)67.710, 67.710, 158.137
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

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Components

#1: Protein Iron dependent repressor, putative /


Mass: 15921.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_2539 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RRF3
#2: DNA chain DNA (5'-D(*TP*AP*TP*TP*TP*TP*AP*GP*GP*CP*GP*CP*GP*AP*CP*TP*AP*AP*AP*AP*T)-3')


Mass: 6461.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Deinococcus radiodurans (radioresistant)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 4.05 Å3/Da / Density % sol: 69.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 8K 26% (w/v); Imidazole 0.1 M pH 7.8; NaCl 0.2 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→47.88 Å / Num. obs: 19507 / % possible obs: 100 % / Redundancy: 8.8 % / Biso Wilson estimate: 47.2 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.32 Å / Num. unique obs: 2768 / CC1/2: 0.678

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.88 Å / SU ML: 0.2956 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 24.6276
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2273 1855 5.2 %
Rwork0.1826 33798 -
obs0.1849 19456 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 733 10 92 1875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082034
X-RAY DIFFRACTIONf_angle_d1.09532940
X-RAY DIFFRACTIONf_chiral_restr0.0505333
X-RAY DIFFRACTIONf_plane_restr0.0097235
X-RAY DIFFRACTIONf_dihedral_angle_d27.058564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.3581660.31642618X-RAY DIFFRACTION100
2.26-2.330.30691400.28032585X-RAY DIFFRACTION99.93
2.33-2.40.31131810.2672543X-RAY DIFFRACTION99.96
2.4-2.490.27851180.26842623X-RAY DIFFRACTION100
2.49-2.590.33581270.28232594X-RAY DIFFRACTION99.85
2.59-2.70.27851540.24112607X-RAY DIFFRACTION100
2.7-2.850.26651460.22892592X-RAY DIFFRACTION100
2.85-3.020.25221170.22672627X-RAY DIFFRACTION99.93
3.03-3.260.26991340.20842593X-RAY DIFFRACTION99.82
3.26-3.590.23371650.1672590X-RAY DIFFRACTION99.89
3.59-4.10.18561300.14932603X-RAY DIFFRACTION100
4.11-5.170.16171250.12872622X-RAY DIFFRACTION100
5.17-47.880.18911520.14552601X-RAY DIFFRACTION99.75
Refinement TLS params.Method: refined / Origin x: 165.387361857 Å / Origin y: 26.3545742634 Å / Origin z: 191.345649293 Å
111213212223313233
T0.238204876802 Å2-0.0132983928193 Å20.00342548619065 Å2-0.155579791082 Å2-0.028347693085 Å2--0.162669862333 Å2
L1.78111648742 °20.635906344063 °20.042292027238 °2-1.00841893823 °2-0.450559812934 °2--0.954909746576 °2
S-0.183081649289 Å °0.0707509238441 Å °0.0444132483434 Å °0.0515982719658 Å °0.161429862191 Å °-0.0676875349643 Å °-0.0682763056795 Å °0.0892425271579 Å °-0.0174428194597 Å °
Refinement TLS groupSelection details: all

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