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- PDB-6rmq: Crystal structure of a selenomethionine-substituted A70M I84M mut... -

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Basic information

Entry
Database: PDB / ID: 6rmq
TitleCrystal structure of a selenomethionine-substituted A70M I84M mutant 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 / 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
Similarity search - Domain/homology
HTH-type transcriptional regulator DdrOC
Similarity search - Component
Biological speciesDeinococcus deserti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 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 7, 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 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)29,9552
Polymers29,9552
Non-polymers00
Water77543
1
A: HTH-type transcriptional regulator DdrOC

A: HTH-type transcriptional regulator DdrOC


Theoretical massNumber of molelcules
Total (without water)29,9552
Polymers29,9552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area1780 Å2
ΔGint-8 kcal/mol
Surface area15470 Å2
MethodPISA
2
B: HTH-type transcriptional regulator DdrOC

B: HTH-type transcriptional regulator DdrOC


Theoretical massNumber of molelcules
Total (without water)29,9552
Polymers29,9552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area1810 Å2
ΔGint-13 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.450, 76.980, 131.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein HTH-type transcriptional regulator DdrOC


Mass: 14977.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus deserti (bacteria) / Gene: ddrOC, Deide_20570 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: C1CYP4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 3.5 M Ammonium Chloride 0.1 M Bis-Tris propane pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 3→76 Å / Num. obs: 7531 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.5
Reflection shellResolution: 3→3.3 Å / Num. unique obs: 1193

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
SCALAdata scaling
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 3→76 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.834 / SU B: 18.346 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28382 405 5.4 %RANDOM
Rwork0.19745 ---
obs0.20206 7098 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.768 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 3→76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 0 0 43 2025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192016
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9612.0042724
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4955240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.01922.596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.99315372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6441526
X-RAY DIFFRACTIONr_chiral_restr0.1320.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211500
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_it1.7382.641972
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0053.9551208
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4092.8921043
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.63535.4332961
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: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 33 -
Rwork0.233 516 -
obs--100 %

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