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- PDB-8sbh: YeiE effector binding domain from E. coli -

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Basic information

Entry
Database: PDB / ID: 8sbh
TitleYeiE effector binding domain from E. coli
ComponentsTranscriptional regulator YeiE, LysR family
KeywordsDNA BINDING PROTEIN / LysR-type transcriptional regulator / LTTR / sulfur metabolism / sulfite / cysteine biosynthesis
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA-templated transcription / regulation of DNA-templated transcription
Similarity search - Function
: / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Uncharacterized HTH-type transcriptional regulator YeiE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsMomany, C. / Nune, M. / Brondani, J.C. / Afful, D. / Neidle, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1024108 United States
Citation
Journal: To Be Published
Title: FinR, a LysR-type transcriptional regulator involved in sulfur homeostasis with homologs in diverse microorganisms
Authors: Momany, C. / Nune, M. / Brondani, J.C. / Afful, D. / Neidle, E.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: 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
DepositionApr 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator YeiE, LysR family
B: Transcriptional regulator YeiE, LysR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,85716
Polymers47,6132
Non-polymers1,24514
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.098, 71.098, 196.336
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
Components on special symmetry positions
IDModelComponents
11B-436-

HOH

21B-502-

HOH

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Components

#1: Protein Transcriptional regulator YeiE, LysR family


Mass: 23806.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: yeiE, b2157, JW2144 / Plasmid: pET28b(+).SapKO-CH.YeiE_EBD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ACR4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 6.5
Details: YeiE-EBD was dialyzed into 20 mM TRIS, 10 mM mercaptolethanol, pH 8.0 . 2 mcl protein was mixed with 2 mcl Hampton Research Index cocktail 30 HR-IN-30 (0.1 M sodium chloride, 0.1 M BIS-TRIS ...Details: YeiE-EBD was dialyzed into 20 mM TRIS, 10 mM mercaptolethanol, pH 8.0 . 2 mcl protein was mixed with 2 mcl Hampton Research Index cocktail 30 HR-IN-30 (0.1 M sodium chloride, 0.1 M BIS-TRIS pH 6.5, 1.5 M ammonium sulfate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 19, 2016 / Details: Insertion device
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→100 Å / Num. obs: 38819 / % possible obs: 99.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 22.91 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.043 / Rrim(I) all: 0.078 / Χ2: 0.789 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.93-1.963.20.44418920.820.9490.2910.5340.62199.9
1.96-23.20.35818770.8750.9660.2360.4310.598100
2-2.043.20.28719380.9060.9750.190.3450.613100
2.04-2.083.20.26218890.9170.9780.1710.3140.645100
2.08-2.123.20.21719270.9520.9880.1430.2610.648100
2.12-2.173.20.19219070.9580.9890.1260.2310.654100
2.17-2.233.20.18319290.960.990.120.220.639100
2.23-2.293.20.15819210.9680.9920.1040.190.678100
2.29-2.363.20.13719070.9750.9940.090.1650.713100
2.36-2.433.20.12319280.9830.9960.0810.1470.679100
2.43-2.523.20.11219370.9850.9960.0730.1340.709100
2.52-2.623.20.10319350.9840.9960.0670.1230.732100
2.62-2.743.20.09319410.9860.9960.0610.1120.829100
2.74-2.883.20.0819410.990.9970.0530.0960.934100
2.88-3.063.20.06619520.9930.9980.0440.081.003100
3.06-3.33.20.05419560.9950.9990.0360.0650.994100
3.3-3.633.20.04219870.9960.9990.0280.0511.009100
3.63-4.163.20.03520000.9970.9990.0230.0421.031100
4.16-5.243.10.03120300.99810.020.0380.97399.8
5.24-10030.03420250.9970.9990.0220.0411.06891.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→31.8 Å / SU ML: 0.1269 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.0928
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1119 2.89 %5%
Rwork0.1664 37549 --
obs0.1669 38668 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.31 Å2
Refinement stepCycle: LAST / Resolution: 1.93→31.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 76 349 3595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343360
X-RAY DIFFRACTIONf_angle_d0.61734551
X-RAY DIFFRACTIONf_chiral_restr0.0437504
X-RAY DIFFRACTIONf_plane_restr0.0048579
X-RAY DIFFRACTIONf_dihedral_angle_d13.35831265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.020.22311360.21314622X-RAY DIFFRACTION99.87
2.02-2.120.19191380.18354610X-RAY DIFFRACTION99.87
2.12-2.260.18751380.16874616X-RAY DIFFRACTION99.92
2.26-2.430.20541390.15984661X-RAY DIFFRACTION99.85
2.43-2.680.19721390.17154674X-RAY DIFFRACTION99.98
2.68-3.060.18521410.16574714X-RAY DIFFRACTION99.92
3.06-3.860.17111420.14434775X-RAY DIFFRACTION99.98
3.86-31.80.16441460.17074877X-RAY DIFFRACTION96.84
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)
11.992158927050.773086290966-1.767118602056.19039079101-3.546942438853.18187281701-0.01380683566210.09188796916650.0631741492285-0.001343695433870.0508604753078-0.0243915656358-0.2130320301330.0995891040734-0.09214059887070.132361467605-0.0383686320493-0.01930810704320.155675923985-0.0115872011750.059109351317945.974741932650.273342480166.2312713017
21.930056637733.35406734296-2.023509588497.90174437551-2.33520540442.91761033642-0.04146123768070.0651342450746-0.1225765491130.227829026530.0108260218439-1.19323124174-0.05390028341.277223777420.01141852296260.182759991652-0.0802393696583-0.01962575511040.461403247677-0.01522187287280.3222007773657.597864765646.866192228366.7629749075
30.9472214416821.3772452181-0.3619915349154.42402583743-0.08025237940111.61026455477-0.1719364713790.1999844339670.109165409248-0.474489467880.2111697024910.16283463783-0.2487615048150.0857504363039-0.06709034476750.208154890417-0.0642950979617-0.03445992928780.2064971531070.01482132633890.12236576619442.187489834951.609550064260.3125144396
49.615088459446.34755805163.185004877617.499059827885.594177197644.824632076260.4998540970470.140273512198-0.6164066391170.1713040135220.0299431560354-0.04420930701181.79992383960.179072027895-0.5151771883420.402149842575-0.0674240683476-0.03074388579240.1919895044740.0132131261870.23457598177128.763843811721.305392535365.079250102
58.451887073927.744053452483.935088978199.154104778015.626345098359.279720293990.0519036912269-0.006393226417590.1521186494870.00811207026805-0.1008197423260.262984837807-0.0141006967518-0.8122872103860.08930218701990.118133534807-0.0238671952273-0.01182904776530.2761002299460.02538011880430.13988417241624.617219762535.673886614363.575326379
66.074105428231.152067945273.818575532874.903660213694.767871206856.41487953208-0.148764647771-0.03394579965090.128444333864-0.315942164971-0.2127028671290.404615671121-0.35746331456-1.002024114270.2242186940680.1852779335-0.0168845194915-0.02556142997150.277620232160.02774817397810.17895043363725.031164023238.705646135161.0402059433
78.332651253876.52772281254-1.379344554575.69259577796-1.181219896368.641340413390.260714008537-0.234665557451-0.2321560545690.414963358609-0.2210577563840.01290860679440.215926061338-0.009823062957340.01500369562720.120183599594-0.020471626275-0.008511749698260.114139739936-0.01052765284870.099883922107531.902816488333.857786448573.5987938007
82.379656140381.048530388162.072173067153.457728372191.301644408288.69880479297-0.01578661481510.124589858491-0.315386281495-0.1371519757710.167899176008-0.1668894685480.5767564893270.103370485288-0.1597270323550.164358860392-0.03275031671340.009813931138550.131266937265-0.02494517342610.12120662900837.518592545329.695657934763.2465166562
91.919292828841.983102872780.8845254646879.143125737551.595127675722.07507306987-0.1874323902380.3146159548150.110752057447-0.4137670937920.135878840286-0.631027946591-0.4377476363460.219006362930.02423573712570.332457968972-0.160041006493-0.01981954028450.3448877313090.03566631183010.1503229028643.882371071352.720016202254.0748156284
102.295473417480.107873540029-0.1658154542777.09115876382-0.05102440857487.25815168704-0.2969093037911.5729907344-0.257573875741-1.220227144730.28621103881-0.7718161449950.1644566395990.357518262649-0.1726675752750.372050643711-0.04956989638770.1187264292720.613823719716-0.06912887814380.30936130993356.679335611850.790618435257.2759399202
117.319279356991.145991817570.4054490931493.485047551570.5182658772842.76857101781-0.008683850380810.675578971925-0.608784426316-0.33242186855-0.4989579714090.4973894596730.252677122074-1.40180977760.2381620028930.158033338022-0.0633898703947-0.01913168181030.579156837698-0.1929091213620.25482508500926.021016334438.141876958281.9128465499
123.74876849635-1.75254890197-0.153838317472.67945324872-1.33508219673.593796688340.4968003281690.6033480354730.126289763072-0.138514244108-0.3493648993550.307632576952-0.939079714737-1.069920194910.03990469648240.1894502465240.272111590043-0.003448631764110.573368548039-0.0654064762530.23626556883825.879841420549.600771417784.5271932873
137.190184511-0.990003995776-0.9837486156311.715349118370.1978527418192.38820121023-0.0552975755767-0.244143423331-0.08315576630540.1177878117310.011571174906-0.1458196137810.0002218190054460.08701344307570.03859481212560.157632305531-0.00878116007705-0.04023131761840.0993719547239-0.008138731465220.060407021222150.709710294842.471546392787.8216660157
145.33719106681-5.074805273615.67964375485.42581373952-5.534911750176.08008819849-0.0355263715667-0.1875538475210.4157679857330.231623861167-0.1290772015160.0428850618972-0.8783267768890.0921156936640.2203228644460.238142867047-0.008149636689540.02748331594640.161723245729-0.01319000244080.13835901125745.307428095352.669521314487.6563882225
152.11167131895-0.4918553566570.1698824711921.993740355840.5046950254122.71567000092-0.00498612919188-0.0907799211938-0.009627584390520.0618108726407-0.04566132425790.0465701563028-0.12651315875-0.01878525415910.05218474145970.103285509941-0.00162069177343-0.01613604089060.1017458230940.0007054909195120.080226485082444.633218700943.795733193185.2868014148
165.180708911743.022811199841.064768745366.43618415307-1.476493917771.200746731160.162817830803-1.53339865335-0.2392601758981.96143587435-0.9404240285220.7750607504430.307105048977-0.7566777320680.5669044328551.14345112664-0.6006027469380.366066095831.11815321535-0.2865990862050.75697706752220.27334755137.085346071191.1356115239
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 90 through 103 )AA90 - 1031 - 14
22chain 'A' and (resid 104 through 114 )AA104 - 11415 - 25
33chain 'A' and (resid 115 through 166 )AA115 - 16626 - 77
44chain 'A' and (resid 167 through 179 )AA167 - 17978 - 90
55chain 'A' and (resid 180 through 195 )AA180 - 19591 - 106
66chain 'A' and (resid 196 through 220 )AA196 - 220107 - 131
77chain 'A' and (resid 221 through 234 )AA221 - 234132 - 145
88chain 'A' and (resid 235 through 260 )AA235 - 260146 - 171
99chain 'A' and (resid 261 through 276 )AA261 - 276172 - 187
1010chain 'A' and (resid 277 through 288 )AA277 - 288188 - 199
1111chain 'B' and (resid 90 through 114 )BB90 - 1141 - 25
1212chain 'B' and (resid 115 through 152 )BB115 - 15226 - 63
1313chain 'B' and (resid 153 through 190 )BB153 - 19064 - 101
1414chain 'B' and (resid 191 through 204 )BB191 - 204102 - 115
1515chain 'B' and (resid 205 through 276 )BB205 - 276116 - 187
1616chain 'B' and (resid 277 through 288 )BB277 - 288188 - 199

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