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- PDB-6xiv: SeMet-Rns, in complex with potential inhibitor -

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Basic information

Entry
Database: PDB / ID: 6xiv
TitleSeMet-Rns, in complex with potential inhibitor
ComponentsRegulatory protein Rns
KeywordsDNA BINDING PROTEIN/INHIBITOR / Rns / ETEC / transcription factor / inhibitor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / cytoplasm
Similarity search - Function
Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeobox-like domain superfamily
Similarity search - Domain/homology
DECANOIC ACID / (2S)-2-hydroxybutanedioic acid / Regulatory protein Rns
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMidgett, C.R. / Kull, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI060031 United States
CitationJournal: Sci Rep / Year: 2021
Title: Structure of the master regulator Rns reveals an inhibitor of enterotoxigenic Escherichia coli virulence regulons.
Authors: Midgett, C.R. / Talbot, K.M. / Day, J.L. / Munson, G.P. / Kull, F.J.
History
DepositionJun 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein Rns
B: Regulatory protein Rns
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3445
Polymers62,8652
Non-polymers4793
Water0
1
A: Regulatory protein Rns
hetero molecules

B: Regulatory protein Rns
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3445
Polymers62,8652
Non-polymers4793
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area2530 Å2
ΔGint5 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.510, 49.970, 102.920
Angle α, β, γ (deg.)90.000, 106.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 8 through 263)
21(chain B and (resid 8 through 95 or resid 98 through 263))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and resid 8 through 263)A8 - 263
211(chain B and (resid 8 through 95 or resid 98 through 263))B8 - 95
221(chain B and (resid 8 through 95 or resid 98 through 263))B98 - 263

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Components

#1: Protein Regulatory protein Rns


Mass: 31432.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: ETEC / Gene: rns / Production host: Escherichia coli (E. coli) / Strain (production host): B834 DE3 / References: UniProt: P16114
#2: Chemical ChemComp-DKA / DECANOIC ACID / Capric acid


Mass: 172.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M malic acid pH 7, 6% PEG 3350, 0.01 M Betaine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979184 Å / Relative weight: 1
ReflectionResolution: 2.8→29.2884 Å / Num. obs: 17538 / % possible obs: 94.93 % / Redundancy: 13 % / Biso Wilson estimate: 89.24 Å2 / CC1/2: 0.995 / Net I/σ(I): 8.67
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 1743 / CC1/2: 0.29

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.2884 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 37.49 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2999 1679 9.92 %
Rwork0.2423 15238 -
obs0.2482 16917 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 235.62 Å2 / Biso mean: 93.971 Å2 / Biso min: 46.65 Å2
Refinement stepCycle: final / Resolution: 2.8→29.2884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4189 0 33 0 4222
Biso mean--89.13 --
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074281
X-RAY DIFFRACTIONf_angle_d0.9265739
X-RAY DIFFRACTIONf_dihedral_angle_d14.8532644
X-RAY DIFFRACTIONf_chiral_restr0.052660
X-RAY DIFFRACTIONf_plane_restr0.004712
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2329X-RAY DIFFRACTION8.196TORSIONAL
12B2329X-RAY DIFFRACTION8.196TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.88230.48221270.4008114186
2.8823-2.97530.41251190.3671116789
2.9753-3.08150.48011280.3625120190
3.0815-3.20480.40561340.332122193
3.2048-3.35040.38231380.3284126995
3.3504-3.52680.31271360.2622129697
3.5268-3.74730.30031540.259127998
3.7473-4.0360.31821400.2439131798
4.036-4.44090.29011570.2238130398
4.4409-5.08060.25451390.1892133299
5.0806-6.390.3021530.2502134299
6.39-29.28840.25721540.2098137098

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