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- PDB-6rnz: Crystal structure of the N-terminal HTH DNA-binding domain of the... -

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Basic information

Entry
Database: PDB / ID: 6rnz
TitleCrystal structure of the N-terminal HTH DNA-binding domain of the essential repressor DdrO from radiation-resistant Deinococcus bacteria (Deinococcus deserti)
ComponentsHTH-type transcriptional regulator DdrOC
KeywordsDNA BINDING PROTEIN / ----
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / Helix-turn-helix / lambda repressor-like DNA-binding domains / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional regulator DdrOC
Similarity search - Component
Biological speciesDeinococcus deserti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsArnoux, P. / Siponen, M.I. / Pignol, D. / Brandelet, G. / 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 10, 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 / refine / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _software.name

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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)15,3015
Polymers15,0252
Non-polymers2763
Water4,594255
1
A: HTH-type transcriptional regulator DdrOC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7894
Polymers7,5131
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HTH-type transcriptional regulator DdrOC


Theoretical massNumber of molelcules
Total (without water)7,5131
Polymers7,5131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.257, 43.227, 45.870
Angle α, β, γ (deg.)90.00, 106.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HTH-type transcriptional regulator DdrOC


Mass: 7512.542 Da / Num. of mol.: 2 / Fragment: N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus deserti (bacteria) / Gene: ddrOC, Deide_20570
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C1CYP4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 49.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris propane pH 7, 2.5 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.35→44 Å / Num. obs: 31092 / % possible obs: 98.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.9
Reflection shellResolution: 1.35→1.4 Å / Num. unique obs: 2968

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RNX

6rnx


Resolution: 1.35→43.94 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.038 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17701 1558 5 %RANDOM
Rwork0.1287 ---
obs0.13114 29520 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.675 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.31 Å2
2---0.23 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.35→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 18 255 1327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0191147
X-RAY DIFFRACTIONr_bond_other_d0.0020.021132
X-RAY DIFFRACTIONr_angle_refined_deg2.3752.0211561
X-RAY DIFFRACTIONr_angle_other_deg1.47732626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2425150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90523.21456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59415222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0051515
X-RAY DIFFRACTIONr_chiral_restr0.1590.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021266
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02221
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_it1.6941.082551
X-RAY DIFFRACTIONr_mcbond_other1.691.081550
X-RAY DIFFRACTIONr_mcangle_it1.9091.632691
X-RAY DIFFRACTIONr_mcangle_other1.9091.632692
X-RAY DIFFRACTIONr_scbond_it3.8971.613596
X-RAY DIFFRACTIONr_scbond_other3.9031.611596
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.552.242861
X-RAY DIFFRACTIONr_long_range_B_refined6.15617.7041420
X-RAY DIFFRACTIONr_long_range_B_other6.15417.7161421
X-RAY DIFFRACTIONr_rigid_bond_restr5.47332279
X-RAY DIFFRACTIONr_sphericity_free38.9795156
X-RAY DIFFRACTIONr_sphericity_bonded12.85652360
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 118 -
Rwork0.242 2085 -
obs--95.66 %

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