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- PDB-8bt1: YdaT transcription regulator (CII functional analog) -

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Basic information

Entry
Database: PDB / ID: 8bt1
TitleYdaT transcription regulator (CII functional analog)
ComponentsYdaT_toxin domain-containing protein
KeywordsDNA BINDING PROTEIN / CII functional analog / prophage CP-9339
Function / homologyBacterial toxin YdaT / Bacterial toxin YdaT superfamily / Bacterial toxin ydaT / YdaT_toxin domain-containing protein
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39788433003 Å
AuthorsProlic-Kalinsek, M. / Loris, R.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G.0226.17N Belgium
Research Foundation - Flanders (FWO)G.0033.20N Belgium
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7.
Authors: Prolic-Kalinsek, M. / Volkov, A.N. / Hadzi, S. / Van Dyck, J. / Bervoets, I. / Charlier, D. / Loris, R.
#1: Journal: mBio / Year: 2021
Title: Bistable Expression of a Toxin-Antitoxin System Located in a Cryptic Prophage of Escherichia coli O157:H7.
Authors: Jurenas, D. / Fraikin, N. / Goormaghtigh, F. / De Bruyn, P. / Vandervelde, A. / Zedek, S. / Jove, T. / Charlier, D. / Loris, R. / Van Melderen, L.
History
DepositionNov 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YdaT_toxin domain-containing protein
B: YdaT_toxin domain-containing protein
C: YdaT_toxin domain-containing protein
D: YdaT_toxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3679
Polymers74,0164
Non-polymers3515
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-70 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.570, 64.256, 63.910
Angle α, β, γ (deg.)66.830, 89.360, 77.672
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPROPRO(chain 'A' and ((resid 2 and (name N or name...AA2 - 6723 - 88
12ALAALAGLUGLU(chain 'A' and ((resid 2 and (name N or name...AA69 - 7190 - 92
13GLNGLNGLUGLU(chain 'A' and ((resid 2 and (name N or name...AA74 - 10595 - 126
14ARGARGVALVAL(chain 'A' and ((resid 2 and (name N or name...AA107 - 123128 - 144
25LYSLYSPROPRO(chain 'B' and (resid 2 through 3 or (resid 4...BB2 - 6723 - 88
26ALAALAGLUGLU(chain 'B' and (resid 2 through 3 or (resid 4...BB69 - 7190 - 92
27GLNGLNGLUGLU(chain 'B' and (resid 2 through 3 or (resid 4...BB74 - 10595 - 126
28ARGARGVALVAL(chain 'B' and (resid 2 through 3 or (resid 4...BB107 - 123128 - 144
39LYSLYSPROPRO(chain 'C' and ((resid 2 and (name N or name...CC2 - 6723 - 88
310ALAALAGLUGLU(chain 'C' and ((resid 2 and (name N or name...CC69 - 7190 - 92
311GLNGLNGLUGLU(chain 'C' and ((resid 2 and (name N or name...CC74 - 10595 - 126
312ARGARGVALVAL(chain 'C' and ((resid 2 and (name N or name...CC107 - 123128 - 144
413LYSLYSPROPRO(chain 'D' and (resid 2 through 5 or (resid 6...DD2 - 6723 - 88
414ALAALAGLUGLU(chain 'D' and (resid 2 through 5 or (resid 6...DD69 - 7190 - 92
415GLNGLNGLUGLU(chain 'D' and (resid 2 through 5 or (resid 6...DD74 - 10595 - 126
416ARGARGVALVAL(chain 'D' and (resid 2 through 5 or (resid 6...DD107 - 123128 - 144

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Components

#1: Protein
YdaT_toxin domain-containing protein


Mass: 18504.076 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: Z6071 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6M7H0F8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 ul 13.23 mg/ml YdaT (in 20mM Tris and 200mM NaCl, pH 7.5) mixed with 0.1 ul reservoir solution (0.1M BIS - TRIS pH 5.5, 2.0 M Ammonium sulphate) and equilibrated against 70 ul of reservoir solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.39→44.3725791252 Å / Num. obs: 19698 / % possible obs: 77.3981758138 % / Redundancy: 2.3325 % / Biso Wilson estimate: 37.9536592773 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.106 / Net I/σ(I): 6
Reflection shellResolution: 2.4→2.52 Å / Rmerge(I) obs: 0.386 / Num. unique obs: 993 / CC1/2: 0.797 / Rrim(I) all: 0.552

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39788433003→44.3725791252 Å / SU ML: 0.302408743077 / Cross valid method: FREE R-VALUE / σ(F): 1.97085360119 / Phase error: 31.5909210916
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.265817898604 979 4.97282470666 %
Rwork0.211205561502 18708 -
obs0.213955987448 19687 77.3981758138 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.1841727531 Å2
Refinement stepCycle: LAST / Resolution: 2.39788433003→44.3725791252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 19 136 3870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007745293185753847
X-RAY DIFFRACTIONf_angle_d0.9592254376115256
X-RAY DIFFRACTIONf_chiral_restr0.0549449884771603
X-RAY DIFFRACTIONf_plane_restr0.00671038741088682
X-RAY DIFFRACTIONf_dihedral_angle_d13.33142154942351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3979-2.52430.278335121201460.2757260824981188X-RAY DIFFRACTION33.9570720969
2.5243-2.68240.3342782298561080.2712148873971926X-RAY DIFFRACTION55.7718672882
2.6824-2.88950.3146687702161310.2593282542792423X-RAY DIFFRACTION70.8853733
2.8895-3.18020.3208172915721640.2527744491473105X-RAY DIFFRACTION89.7091108672
3.1802-3.64020.2874564552851760.2133463498473351X-RAY DIFFRACTION97.5656984786
3.6402-4.58550.2269287651181780.1777039551533377X-RAY DIFFRACTION96.8664850136
4.5855-44.370.2358339470171760.1960849941713338X-RAY DIFFRACTION97.0450151892
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.49941447797-0.6005674714042.691097473785.30221458724-3.896955155969.047102097930.367208349505-0.2120250353391.118304276710.723105716165-0.4455653362630.496887921867-0.3981860012310.3494953126630.2767032939750.201926016737-0.01511516448530.09116471076260.1966659108670.03497182741360.571967302449-10.9180637407-29.9832939771-9.44117395729
24.2392439423-1.891992959170.6640675514034.60464121758-1.284855953553.344459846360.1576599311580.08586825500830.243421274260.0574282631005-0.2204199310080.0104065272691-0.08644133213420.1029820965440.05308819817720.0509414911764-0.0358162362883-0.01456931414560.172600668869-0.02106852157380.20763424299-21.546674469-36.1612425185-13.184352231
32.29188866976-3.403974788853.130249520845.11000672781-4.758033166574.56146533174-0.1134089811020.298756812174-0.01865858968210.388382382203-0.0539170803238-0.241113610286-0.4496728563960.5328764523770.1640422886560.0638438571046-0.005472936930380.09072697144790.388115384534-0.01387545869890.664028010671-4.39657075759-32.5734290547-14.7373673735
43.65046160498-0.720358627301-0.547094336635.01062034625-1.626700802052.90725251324-0.193865318945-0.161104764782-0.2726176901820.4267120464740.66003136541-0.373384894673-0.313089992828-0.299409415885-0.1731777138620.104644298227-0.0507820888080.1121220853410.302654951654-0.08984931906910.2837883333166.35234552256-21.3865968981-19.837315953
55.656554130611.56538831433-0.8392291837643.311936491810.4565722319134.292971052640.340012215611-0.482363728809-0.0769417092630.253211248992-0.453627414938-0.07872487993920.00668140720486-0.2408999119230.08942449042470.331814810948-0.1018435553130.05436414826220.3737030175570.01723350779470.23694124621523.3705910808-8.46193295612-51.8224445529
60.1616111153270.514362423983-0.4120807029021.65622382192-0.5850277657874.522513676350.389653505512-0.604768180794-0.133792737460.40144667192-0.100227717865-0.0773594828467-0.5993098026750.376282204493-0.1711340867520.415694578744-0.1501478296630.1484302682770.443142505329-0.02120990717780.32605050051225.594105803-6.79956905711-46.6878673677
73.70413823923.58656670908-0.2975242769023.644031808980.4628223408873.222522588680.09930350545860.198296600426-0.364069702150.2247087940440.154073181144-1.31206794487-0.1142242036180.406100172231-0.2748831391180.112052343893-0.002059143986870.003423237968720.286319227403-0.03154174139140.29445248815413.0169125773-23.4703832578-27.7132651774
84.472587463840.0320335782552-0.2177974606416.194223067150.2511125479313.708897492940.206191903634-0.299578809204-0.3564490369310.642811618458-0.260934159713-0.0683686397180.5686217760040.1670570882570.02973810825990.3076978490730.0105982584938-0.01042646317060.1448712879630.006775525681340.2648893360560.4045288802053.4785456437-8.34386767709
94.33506540507-2.696811211381.086681772582.296093895160.1768506083262.890588047180.139540715586-0.05006720690740.250966598669-0.605298648995-0.3017897799090.530054055355-0.426561965838-0.334022984364-0.01282239991970.1991092812180.0523869476215-0.02205762079780.312455314283-0.04796427224920.314772039485-1.57040748987-14.3913422139-27.1830100994
107.936420789080.8535309301970.08647142849467.859180012170.5615966450726.42040061724-0.758163239906-0.574979080016-0.419989571174-1.32011395674-0.182068870188-0.815420257351.566136966020.7140594355420.7937096982290.9212243458390.2297460637370.3034175131470.4706739975240.053990253670.73660260152418.554408298-38.5424977603-43.6453444019
113.73240302104-2.141542082472.81058645042.27742158243-1.929041050642.20044591033-0.153922773259-0.385667510306-1.11740196282-0.7857839431060.158727399187-1.264105421661.133858857250.731644541084-0.3922739794421.560022152350.2597021267820.3408597047581.178437873450.1050971887690.8601194796726.3747889146-47.3034608205-46.5205111939
122.88221095665-1.36814445644-1.022066078942.810084645743.388110427134.23166390168-0.211688317446-0.245533524808-1.13219395823-1.31137035162-0.273809683677-0.3096263621951.862687445550.02395775180770.5276670870251.331104336630.1224974887050.345472422150.480632189061-0.1146932747650.76168541314512.9773152724-43.1523735008-41.023193055
136.285301282022.8452944216-0.3826543846794.28634870645-1.331478632755.38952719794-0.1705461721890.8190058634850.0676032644377-1.228182219130.2439845082980.749899695996-0.1606269813370.187025517572-0.008703965811130.321175553016-0.0567997970580.01688282602950.390350332244-0.05762883772370.1964806105015.00749844759-19.9772660748-35.2358683781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 97 )
4X-RAY DIFFRACTION4chain 'A' and (resid 98 through 124 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 49 )
6X-RAY DIFFRACTION6chain 'B' and (resid 50 through 97 )
7X-RAY DIFFRACTION7chain 'B' and (resid 98 through 128 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 92 )
9X-RAY DIFFRACTION9chain 'C' and (resid 93 through 123 )
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 33 )
11X-RAY DIFFRACTION11chain 'D' and (resid 34 through 66 )
12X-RAY DIFFRACTION12chain 'D' and (resid 67 through 97 )
13X-RAY DIFFRACTION13chain 'D' and (resid 98 through 127 )

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