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

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Basic information

Entry
Database: PDB / ID: 8pvz
TitleManganese-dependent transcriptional repressor DR2539 complexed with cadmium
ComponentsIron 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 / cytoplasm
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 ...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
: / Manganese transport regulator
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJul 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 19, 2025Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_struct_assembly_gen / pdbx_struct_oper_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron dependent repressor, putative
B: Iron dependent repressor, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,31724
Polymers31,8442
Non-polymers2,47322
Water2,504139
1
A: Iron dependent repressor, putative
B: Iron dependent repressor, putative
hetero molecules

A: Iron dependent repressor, putative
B: Iron dependent repressor, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,63448
Polymers63,6884
Non-polymers4,94644
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)60.785, 60.785, 187.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Iron dependent repressor, putative


Mass: 15921.969 Da / Num. of mol.: 2
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: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 3% 6-Aminohexanoic acid; 0.1M Hepes pH 7.0; 1.2 M sodium acetate; 0.05M Cadmium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97933 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2→46.92 Å / Num. obs: 24727 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 35.33 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.11 Å / Num. unique obs: 3534 / CC1/2: 0.622

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.6 Å / SU ML: 0.2513 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.7527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22 1203 4.88 %
Rwork0.1856 23440 -
obs0.1873 24643 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.42 Å2
Refinement stepCycle: LAST / Resolution: 2→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 22 139 2240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132139
X-RAY DIFFRACTIONf_angle_d1.18542913
X-RAY DIFFRACTIONf_chiral_restr0.0653335
X-RAY DIFFRACTIONf_plane_restr0.0095384
X-RAY DIFFRACTIONf_dihedral_angle_d4.9227299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.30631250.27462539X-RAY DIFFRACTION99.89
2.08-2.170.28051240.2212566X-RAY DIFFRACTION99.74
2.17-2.290.21011330.18142556X-RAY DIFFRACTION99.81
2.29-2.430.24551320.18522585X-RAY DIFFRACTION99.96
2.43-2.620.23491320.18522562X-RAY DIFFRACTION100
2.62-2.880.22051500.17722586X-RAY DIFFRACTION99.85
2.88-3.30.23971320.18522613X-RAY DIFFRACTION99.82
3.3-4.160.18511350.17182628X-RAY DIFFRACTION99.1
4.16-43.60.21371400.18442805X-RAY DIFFRACTION98.26
Refinement TLS params.Method: refined / Origin x: 86.1323728661 Å / Origin y: 60.4966891884 Å / Origin z: 12.6362827481 Å
111213212223313233
T0.21837344063 Å2-0.0188812179472 Å2-0.00212557414542 Å2-0.263220142675 Å2-0.0146804699837 Å2--0.277774931351 Å2
L0.298740601147 °2-0.000958573661006 °2-0.0310521475663 °2-0.68637919048 °20.758437311323 °2--2.22094518269 °2
S-0.107213521869 Å °-0.0388120174029 Å °-0.0540460132494 Å °0.0553784220739 Å °0.0566249914459 Å °-0.0477720654397 Å °0.0630294221897 Å °0.055672690213 Å °0.0448412293584 Å °
Refinement TLS groupSelection details: all

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