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- PDB-6rnx: Crystal structure of the essential repressor DdrO from radiation-... -

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Basic information

Entry
Database: PDB / ID: 6rnx
TitleCrystal structure of the essential repressor DdrO from radiation-resistant Deinococcus bacteria (Deinococcus deserti)
ComponentsHTH-type transcriptional regulator DdrOC
KeywordsDNA BINDING PROTEIN
Function / homologyHelix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA-binding transcription factor activity / DNA binding / cytosol / HTH-type transcriptional regulator DdrOC
Function and homology information
Biological speciesDeinococcus deserti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsArnoux, P. / Siponen, M.I. / Pignol, D. / De Groot, A. / Blanchard, L.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Crystal structure of the transcriptional repressor DdrO: insight into the metalloprotease/repressor-controlled radiation response in Deinococcus.
Authors: de Groot, A. / Siponen, M.I. / Magerand, R. / Eugenie, N. / Martin-Arevalillo, R. / Doloy, J. / Lemaire, D. / Brandelet, G. / Parcy, F. / Dumas, R. / Roche, P. / Servant, P. / Confalonieri, ...Authors: de Groot, A. / Siponen, M.I. / Magerand, R. / Eugenie, N. / Martin-Arevalillo, R. / Doloy, J. / Lemaire, D. / Brandelet, G. / Parcy, F. / Dumas, R. / Roche, P. / Servant, P. / Confalonieri, F. / Arnoux, P. / Pignol, D. / Blanchard, L.
History
DepositionMay 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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: HTH-type transcriptional regulator DdrOC
B: HTH-type transcriptional regulator DdrOC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5533
Polymers29,5182
Non-polymers351
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, also exists in a dimer / tetramer equilibium (SEC-MALS).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-24 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.902, 130.188, 154.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

#1: Protein HTH-type transcriptional regulator DdrOC


Mass: 14758.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus deserti (strain VCD115 / DSM 17065 / LMG 22923) (bacteria)
Strain: VCD115 / DSM 17065 / LMG 22923 / Gene: ddrOC, Deide_20570
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C1CYP4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris pH 5.5, 0.2 M Na-thiocyanate, 2.3 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 8234 / % possible obs: 99 % / Redundancy: 9.6 % / Biso Wilson estimate: 66.53 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 8.6
Reflection shellResolution: 2.84→2.94 Å / Num. unique obs: 764 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RMQ

6rmq


Resolution: 2.84→49.81 Å / SU ML: 0.5939 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.6037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2958 380 4.63 %RANDOM
Rwork0.2222 7825 --
obs0.2258 8205 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.21 Å2
Refinement stepCycle: LAST / Resolution: 2.84→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 1 15 2044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01052063
X-RAY DIFFRACTIONf_angle_d1.19412789
X-RAY DIFFRACTIONf_chiral_restr0.0509316
X-RAY DIFFRACTIONf_plane_restr0.006358
X-RAY DIFFRACTIONf_dihedral_angle_d4.02991272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-3.260.43041330.29932534X-RAY DIFFRACTION98.85
3.26-4.10.32441170.23012594X-RAY DIFFRACTION99.71
4.1-49.810.24581300.19662697X-RAY DIFFRACTION99.54
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.753951025390.6069027382450.6337566335971.13640242471-0.8743741369781.583930578180.1151570113950.2751330951530.235583068820.1185399574390.215466462746-0.337622527411-0.3033841920960.5864530452920.001739800211080.3849414163560.0617287999706-0.007079945699690.5453344684550.0330110009270.445067009727.08145013672-21.9308267612-12.3972409733
2-0.1361232030621.78499393943-0.03203975010013.966481405932.113246910010.503060800710.184040822716-0.09938278661680.0217939669838-0.319582558364-0.368782868947-0.1057746344310.0361647563795-0.1202191722760.003252030348530.5309426937040.101998457754-0.1385231026370.452685318724-0.06845409233380.575037777286-8.71208275484-48.1324690557-23.6940926736
34.504197188471.39635535963-0.4978879324832.841581045260.4309686979953.455126220310.0754993523161-0.07386983702990.0750862105093-0.171958238955-0.133240041620.0436180853220.0875091473313-0.4389232005760.001862348835820.4554375474160.0232117873545-0.02309748945380.46217702804-0.06303751484620.501279458504-9.91802465195-43.311423746-12.2411285063
43.342524084640.6957044671440.6766370535642.55045786877-1.355957698722.27894036328-0.0166320697755-0.1983058263640.02212210299580.08164604243090.02236075597090.05266478943780.375888828899-0.09330223157530.0006905148104980.5519974302550.1243536678270.03185427603080.4726190109320.02766176292380.4179698426480.778918559306-10.1895905826-27.7595366955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:37)
2X-RAY DIFFRACTION2(chain A and resid 38:129)
3X-RAY DIFFRACTION3(chain B and resid 1:68)
4X-RAY DIFFRACTION4(chain B and resid 69:128)

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