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- PDB-6xiu: ETEC Rns bound to a potential inhibitor, decanoic acid -

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Basic information

Entry
Database: PDB / ID: 6xiu
TitleETEC Rns bound to a potential inhibitor, decanoic acid
ComponentsRegulatory protein Rns
KeywordsDNA BINDING PROTEIN/INHIBITOR / Inhibitor / AraC / ETEC / Virulence / transcription factor / 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 / Regulatory protein Rns
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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)62,0844
Polymers61,7402
Non-polymers3452
Water0
1
A: Regulatory protein Rns
hetero molecules

B: Regulatory protein Rns
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0844
Polymers61,7402
Non-polymers3452
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area2700 Å2
ΔGint5 kcal/mol
Surface area25770 Å2
Unit cell
Length a, b, c (Å)48.240, 95.150, 133.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 9 through 93 or resid 103 through 263))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSLYSA1 - 246
d_21ens_1LYSGLYB1 - 85
d_22ens_1ARGLYSB88 - 248

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Components

#1: Protein Regulatory protein Rns


Mass: 30869.822 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 BL21(DE3) (bacteria) / 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
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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M succinnic acid, 14% PEG 3350, 0.03 M glycyl-glycyl-gylcine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979351 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979351 Å / Relative weight: 1
ReflectionResolution: 2.999→27.39 Å / Num. obs: 12803 / % possible obs: 99.18 % / Redundancy: 6.4 % / Biso Wilson estimate: 93.91 Å2 / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 7.29
Reflection shellResolution: 3→3.107 Å / Num. unique obs: 1219 / CC1/2: 0.549 / CC star: 0.842

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet-Rns

Resolution: 3→27.39 Å / SU ML: 0.5667 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.8516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The crystal has a pseudotranslational symmetry peak at fractional coordinates of 0.00 0.50 0.36 that is 45.7% of the origin peak from Patterson analysis.
RfactorNum. reflection% reflectionSelection details
Rfree0.3017 1279 10.03 %Random selection
Rwork0.2566 11472 --
obs0.2611 12751 99.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.91 Å2
Refinement stepCycle: LAST / Resolution: 3→27.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 24 0 4068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01234126
X-RAY DIFFRACTIONf_angle_d1.35835528
X-RAY DIFFRACTIONf_chiral_restr0.0718636
X-RAY DIFFRACTIONf_plane_restr0.0077682
X-RAY DIFFRACTIONf_dihedral_angle_d19.78131584
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.666736622419 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.120.45131340.43391209X-RAY DIFFRACTION96.83
3.12-3.260.36721410.34461257X-RAY DIFFRACTION99.5
3.26-3.430.37431400.30591260X-RAY DIFFRACTION99.36
3.43-3.650.32141400.29681254X-RAY DIFFRACTION99.57
3.65-3.930.30051400.27151260X-RAY DIFFRACTION99.57
3.93-4.320.26871420.24081274X-RAY DIFFRACTION99.58
4.32-4.940.27961430.21541278X-RAY DIFFRACTION99.58
4.95-6.220.32161450.27141304X-RAY DIFFRACTION99.86
6.22-28.630.27411540.22031376X-RAY DIFFRACTION99.29
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.21544454013-0.540448111145-1.959969307642.44661608328-1.176897885094.859418478990.116131898836-0.02517968235310.00413124036465-0.3176382754930.01738012166140.00251313023343-0.0956960750855-0.0946529871435-0.1093544566070.535532027167-0.0713535701895-0.02306289207740.497308186157-0.0742218181330.456887336842-14.6984624648-6.978118162037.13104502453
21.764615186091.38194746024-1.147950570051.87281298888-0.4613870633774.03188224773-0.2959941222640.217426712525-0.0435918301441-1.26109028128-0.126672615975-0.5494191104040.378013019803-0.3513155716380.4492633415450.9964632982750.1122809502710.1790150726310.7931805773030.03083477054330.773241513018-11.5299673349-4.97734648555-3.10730130099
32.28543275456-0.290120961585-0.1001075228493.977367352551.616888460682.306790504380.060517578016-0.1024887405150.276260206016-0.339666486744-0.0497263937526-0.157840983824-0.3766162785520.004341452196580.1004914130040.4125245029790.01259710032010.03598501491290.5506087502280.01022653886890.563775440846-12.27113876424.6347003252315.8482716169
42.13683243077-0.4244602992191.386691401513.09838397313-1.059211479363.368590606650.284797225357-0.1855837797360.1754332667330.393473818061-0.0956416954860.168956196684-0.36709058938-0.562391435949-0.167228278050.6495008666030.09352651005110.1247200602050.808980811432-0.0859389841010.644667054002-38.4627817267.9916486295340.6575941758
53.43965175819-0.54009727070.9173975370673.436641726831.748968695423.938463327550.02453923645250.2111243919890.2787011860351.18282317401-0.6464170965070.2087831967530.378123301344-0.3629669731210.4058115304220.769420662204-0.169260586134-0.2374745193490.7614509793730.2242418314150.65799633525-34.00152592721.0070256745648.7344352221
64.03886886026-0.411638681838-0.02434354062753.50830964996-0.2161137688921.686782153870.1689791010140.401909709582-0.59340843988-0.0380530417565-0.4835585496220.5323600589080.074687213046-0.4519813179860.2875472912890.4817081517030.0173906593660.009206940696830.645592265563-0.1332825503170.608215435152-38.0499441071-4.1419509288724.79144277
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 9 through 91 )AA9 - 911 - 83
22chain 'A' and (resid 92 through 129 )AA92 - 12984 - 119
33chain 'A' and (resid 130 through 263 )AA130 - 263120 - 253
44chain 'B' and (resid 9 through 91 )BB9 - 911 - 83
55chain 'B' and (resid 92 through 173 )BB92 - 17384 - 163
66chain 'B' and (resid 174 through 263 )BB174 - 263164 - 253

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