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- PDB-8q90: Halophilic Lrp transcription factor -

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Basic information

Entry
Database: PDB / ID: 8q90
TitleHalophilic Lrp transcription factor
ComponentsAsnC family transcriptional regulator
KeywordsTRANSCRIPTION / Transcription factor / DNA protein binding / Halophilic protein / Regulator / Nitrogen metabolism
Function / homology
Function and homology information


sequence-specific DNA binding
Similarity search - Function
AsnC-type HTH domain profile. / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
AsnC family transcriptional regulator
Similarity search - Component
Biological speciesHaloferax mediterranei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGarcia-Bonete, M.J. / Bonete, M.-J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Other governmentVIGROB_016 Spain
Citation
Journal: Int.J.Biol.Macromol. / Year: 2024
Title: Global Lrp regulator protein from Haloferax mediterranei: Transcriptional analysis and structural characterization.
Authors: Matarredona, L. / Garcia-Bonete, M.J. / Guio, J. / Camacho, M. / Fillat, M.F. / Esclapez, J. / Bonete, M.J.
#1: Journal: Genes (Basel) / Year: 2021
Title: Analysis of Haloferax mediterranei Lrp Transcriptional Regulator
Authors: Matarredona, L. / Camacho, M. / Garcia-Bonete, M.J. / Esquerra, B. / Zafrilla, B. / Esclapez, J. / Bonete, M.J.
History
DepositionAug 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Refinement description / Category: citation / pdbx_initial_refinement_model
Item: _citation.journal_volume / _pdbx_initial_refinement_model.entity_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AsnC family transcriptional regulator
B: AsnC family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)35,6962
Polymers35,6962
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-27 kcal/mol
Surface area13690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.360, 60.000, 87.390
Angle α, β, γ (deg.)90.000, 95.990, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein AsnC family transcriptional regulator


Mass: 17847.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax mediterranei (archaea) / Strain: R4 / Gene: lrp / Plasmid: pTA1992.lrp
Details (production host): The plasmid used for protein overexpression was pTA1992, kindly provided by Dr Thorsten Allers (University of Nottingham, UK). This vector contains pHV2 origin, pyrE2 and ...Details (production host): The plasmid used for protein overexpression was pTA1992, kindly provided by Dr Thorsten Allers (University of Nottingham, UK). This vector contains pHV2 origin, pyrE2 and hdrB markers to allow the selection on media lacking uracil and thymidine, and strong p.syn synthetic promoter for constitutive overexpression of halophilic proteins with a N-terminal His-tag
Production host: Haloferax mediterranei (archaea) / Strain (production host): HM26 / References: UniProt: I3R177
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.37 Å3/Da / Density % sol: 48.19 % / Description: Needdle crystals of 100 um long
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 2:1 protein:reservoir 0.1 M Sodium acetate pH 3.6 0.2 M Ammonium acetate 10% PEG 4000 20% Ethylene glycol
PH range: 3.6-4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2→49.38 Å / Num. obs: 22193 / % possible obs: 97.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 26.68 Å2 / CC1/2: 0.979 / CC star: 0.995 / Rpim(I) all: 0.108 / Rrim(I) all: 0.289 / Net I/σ(I): 4.68
Reflection shellResolution: 2→2.071 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 2168 / CC1/2: 0.679 / CC star: 0.9 / Rrim(I) all: 1.13 / % possible all: 97.13

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSVersion Jan 10, 2022data reduction
XSCALEVersion Jan 10, 2022data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.46 Å / SU ML: 0.2101 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 1110 5.01 %0.05
Rwork0.1988 21064 --
obs0.2 22174 97.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.9 Å2
Refinement stepCycle: LAST / Resolution: 2→43.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 0 284 2480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112221
X-RAY DIFFRACTIONf_angle_d1.43026
X-RAY DIFFRACTIONf_chiral_restr0.0837383
X-RAY DIFFRACTIONf_plane_restr0.0061393
X-RAY DIFFRACTIONf_dihedral_angle_d23.001796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.2821340.25562552X-RAY DIFFRACTION96.58
2.09-2.20.2581380.22862621X-RAY DIFFRACTION97.28
2.2-2.340.25291380.22842607X-RAY DIFFRACTION97.48
2.34-2.520.23661380.22882631X-RAY DIFFRACTION97.78
2.52-2.770.25361370.22432609X-RAY DIFFRACTION98.18
2.77-3.170.23861400.21092643X-RAY DIFFRACTION98.3
3.17-40.18581410.17392681X-RAY DIFFRACTION98.77
4-43.460.2051440.17182720X-RAY DIFFRACTION98.9

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