[English] 日本語
Yorodumi
- PDB-6sy6: TetR in complex with the TetR-binding RNA-aptamer K2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sy6
TitleTetR in complex with the TetR-binding RNA-aptamer K2
Components
  • RNA (36-MER)
  • Tetracycline repressor protein class B from transposon Tn10
KeywordsDNA BINDING PROTEIN / TetR / transcription regulator / aptamer / RNA
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type ...Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Tetracycline repressor protein class B from transposon Tn10
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGrau, F.C. / Muller, Y.A. / Suess, B. / Groher, F. / Jaeger, J.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex.
Authors: Grau, F.C. / Jaeger, J. / Groher, F. / Suess, B. / Muller, Y.A.
History
DepositionSep 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Tetracycline repressor protein class B from transposon Tn10
A: Tetracycline repressor protein class B from transposon Tn10
D: RNA (36-MER)


Theoretical massNumber of molelcules
Total (without water)59,7283
Polymers59,7283
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-34 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.564, 96.564, 119.971
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

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
11LEULEULEULEU(chain 'A' and (resid 4 through 5 or resid 7...AB44
12SERSERTHRTHR(chain 'A' and (resid 4 through 5 or resid 7...AB7 - 407 - 40
13TRPTRPHISHIS(chain 'A' and (resid 4 through 5 or resid 7...AB43 - 4443 - 44
14ASNASNPROPRO(chain 'A' and (resid 4 through 5 or resid 7...AB47 - 6947 - 69
15GLYGLYGLYGLY(chain 'A' and (resid 4 through 5 or resid 7...AB72 - 10272 - 102
16PROPROPROPRO(chain 'A' and (resid 4 through 5 or resid 7...AB105105
17LYSLYSVALVAL(chain 'A' and (resid 4 through 5 or resid 7...AB108 - 145108 - 145
18ASPASPGLNGLN(chain 'A' and (resid 4 through 5 or resid 7...AB148 - 149148 - 149
19GLNGLNVALVAL(chain 'A' and (resid 4 through 5 or resid 7...AB152 - 153152 - 153
110GLYGLYTHRTHR(chain 'A' and (resid 4 through 5 or resid 7...AB181 - 202181 - 202
211LEULEULEULEU(chain 'B' and (resid 4 through 5 or resid 7...BA44
212SERSERTHRTHR(chain 'B' and (resid 4 through 5 or resid 7...BA7 - 407 - 40
213TRPTRPHISHIS(chain 'B' and (resid 4 through 5 or resid 7...BA43 - 4443 - 44
214ASNASNPROPRO(chain 'B' and (resid 4 through 5 or resid 7...BA47 - 6947 - 69
215GLYGLYGLYGLY(chain 'B' and (resid 4 through 5 or resid 7...BA72 - 10272 - 102
216PROPROPROPRO(chain 'B' and (resid 4 through 5 or resid 7...BA105105
217LYSLYSVALVAL(chain 'B' and (resid 4 through 5 or resid 7...BA108 - 145108 - 145
218ASPASPGLNGLN(chain 'B' and (resid 4 through 5 or resid 7...BA148 - 149148 - 149
219GLNGLNVALVAL(chain 'B' and (resid 4 through 5 or resid 7...BA152 - 153152 - 153
220GLYGLYTHRTHR(chain 'B' and (resid 4 through 5 or resid 7...BA181 - 202181 - 202

-
Components

#1: Protein Tetracycline repressor protein class B from transposon Tn10


Mass: 23531.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tetR / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04483
#2: RNA chain RNA (36-MER)


Mass: 12664.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15 % (v/v) pentaerythritol propoxylate (5/4 PO/OH), 0.2 M NaCl, pH 6.0, 0.1 M MES-NaOH

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 17, 2019
RadiationMonochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.9→16.11 Å / Num. obs: 14683 / % possible obs: 99.21 % / Redundancy: 20.3 % / Biso Wilson estimate: 68.05 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.8142 / Rpim(I) all: 0.1837 / Rrim(I) all: 0.835 / Net I/σ(I): 4.6
Reflection shellResolution: 2.9→3.003 Å / Redundancy: 21.4 % / Rmerge(I) obs: 5.662 / Mean I/σ(I) obs: 0.47 / Num. unique obs: 1443 / CC1/2: 0.241 / Rpim(I) all: 1.248 / Rrim(I) all: 5.799 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NS7

2ns7


Resolution: 2.9→16.11 Å / SU ML: 0.651 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.8972
RfactorNum. reflection% reflectionSelection details
Rfree0.2882 739 5.04 %Random selection
Rwork0.2476 ---
obs0.2497 14675 99.95 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 75.31 Å2
Refinement stepCycle: LAST / Resolution: 2.9→16.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 779 0 0 3635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373781
X-RAY DIFFRACTIONf_angle_d0.69685285
X-RAY DIFFRACTIONf_chiral_restr0.0339622
X-RAY DIFFRACTIONf_plane_restr0.004544
X-RAY DIFFRACTIONf_dihedral_angle_d12.98582164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.120.45061430.39132741X-RAY DIFFRACTION99.97
3.12-3.430.34081460.32292758X-RAY DIFFRACTION99.93
3.43-3.920.29191450.25052746X-RAY DIFFRACTION99.93
3.92-4.920.26941460.21572802X-RAY DIFFRACTION100
4.92-16.110.24531590.2072889X-RAY DIFFRACTION99.9
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)
14.037475623853.514120245012.589838706764.36750614353.920087519194.34922197374-0.4041253497630.00487083493575-0.5678048576260.896478307609-0.2636253064040.752802950827-0.1880159081760.917689052152-0.1497431088190.738075613623-0.0730920288004-0.1401438704610.555266350490.008979027063020.51267424616846.94624953172.353648130490.452349796166
25.08833762989-0.124054653318-0.3468067486182.28287540204-1.514907929725.90811447685-0.05814071962450.3403190041581.750631896780.1330908303020.00549487299743-1.21040402005-1.395290730410.410976875085-0.03417780385750.753005881544-0.09913181164560.1163717570350.4876929002260.1011097295050.70265759224537.61906044118.48588532335.5815110797
32.76942566817-0.779166723422-0.909467334052.859535415931.290710383182.77333459304-0.117852250461-0.3058588267530.3440138118710.109644427950.0920469306868-0.6076592669940.1592241387320.1593299801050.2028743627280.557004287594-0.091959161917-0.03397384491010.466668065915-0.02825031767050.99803326319434.4220464862.115890700510.693553869805
41.359627536360.803927407784-0.5193789959742.72439508524-0.9492950424790.323223281108-0.3320058308120.1572344800960.6226787476140.6888474670580.5246035695070.0242485979711.370845168640.51457022101-0.213027608761.29017742562-0.0763900471517-0.3010470771050.7886365373210.03840463106720.62412648994324.8749013034-12.0701509444-13.7043705499
53.17985299170.241677846587-1.898786198353.949913217091.532918140083.63145438816-0.28915829332-0.00938069852311-0.225298687455-0.354595011849-0.5922522280861.640324648340.118966046532-1.218496969920.5934194562320.559187896707-0.00602771171956-0.1249338463810.638696214321-0.0381746639490.99281640501423.02768049687.83299597474-1.29901867161
60.1887184221610.127418347195-0.1910178974890.00263892661385-0.06955150920370.06793315504190.4279393387480.938066656052-0.38074322004-1.10063343872-0.274189054191-0.05666738763151.661767728890.80438563169-0.06684241168431.434755606710.197806385045-0.1805504583421.01150265421-0.158600370451.058509150865.6651023044-37.0093055742-11.0208977843
71.63157842090.9681512013141.324420132284.068557669010.7190348842313.160859420080.594549830352-0.193794529317-0.0890356629606-0.252171627086-0.8426481301250.4092804809890.2494868290470.0710744491709-0.05854146557060.718826105525-0.0552941174826-0.1179232682140.6195620648670.03754034657581.1180739457462.776812992-27.02652037340.352534192776
81.106871341520.873728649221-0.7158106234381.329864039-0.9786120036130.627486508875-0.1655217595410.06609508903961.104274706110.5845194036290.5394410821760.7439293158990.2525719796550.39036353579-0.06068005916610.776092026323-0.0969449714065-0.04165411678740.603581191256-0.05330669368251.0929439032965.3959919491-9.52616727015-0.720735730646
90.758396859089-1.27087595117-0.7095729011142.19587779493-1.135377499770.3262441830630.1901921716340.160819940252-0.435689505816-0.368886981755-0.450291136279-0.07223497322630.2498452593460.2670004627190.3082373265470.688715845787-0.05531195740930.05272036786870.7255735972630.02464136937450.76648135327570.6134082841-17.51042839-10.9392227243
105.101651149290.9604394541031.168060275780.853354681154-1.390737733885.172256574031.018793675380.1230729268780.04468743508260.429613762393-0.4504856648620.5950296970350.2193250795230.586224925609-0.1237656810750.624002631665-0.1014450562620.02290970342360.5670535555020.03523744527030.72816326450372.2105724785-28.7267003504-5.79896013483
110.396343460268-1.061186342030.8814765373692.85297057053-2.231723255172.232950118941.200473226130.2167632051370.8143465762190.4922663488661.516268111711.40139236319-0.729997778686-1.48751198067-0.928325875071.152004425260.373695188988-0.0781114829731.277072373150.4904982601641.8217035337773.9144847988-41.4452818543-9.38244185429
125.629122448370.4195957908920.7928031214162.65366324915-0.7955206925182.02094694477-0.495599520894-0.6144622788060.7878871048870.4425933491340.571903785525-0.990273502165-0.6994478538710.183318281610.1972064290640.732314158882-0.0511245405047-0.05058643749940.579305770512-0.0110489003160.75972838662146.4661480254-23.385296562511.5442998604
136.56863428753-2.79466836299-1.208300005373.46400191995-0.3399171151681.327569747480.410081965906-0.71250594128-0.4572205361920.00768052871492-0.2622885392070.1531150426280.06305242657490.1304088826250.003980051966220.638600129439-0.195684775097-0.1368600997640.4541971759270.006410729669830.66178819455140.0769166326-23.41095778146.91182613182
145.07207638458-1.06083331660.06469170796073.19678242465-2.314153364382.428523879780.422626119122-0.02254621753950.782280508660.45606955427-0.107620486655-0.4555186506910.399050016335-0.397152905644-0.08320585093710.613550634086-0.1909266440240.01042373835450.625913628338-0.1031499087110.20044132966430.0793351944-9.215861465758.84003897822
155.430386714852.429611409540.8449628584484.309674478990.6480316811561.826171646850.0625637093954-0.3974732192760.288676992186-0.1150171304490.1430770475230.589252731310.0471484427563-0.214890738062-0.1421957122830.493247859217-0.09667889423780.02009293655180.4139015658340.1066962524660.70559201611825.9516565546-5.719095075532.0689692161
163.239976714250.973144061167-1.276854887163.03129428095-0.9243369351572.45304751213-0.08887651493430.205797021919-0.4892209614440.4094441006710.236058666779-0.358099964491-0.0296155178703-0.1358329662620.1266405549370.614020796982-0.0492628708422-0.03726001696260.5323727136710.08755438218790.31329395458956.96413932630.812280766654-13.1235002746
172.89810933530.208833111471-2.483953552923.22255803119-2.033513356886.77688725332-0.533180956875-0.661657692747-1.39515053412-0.835744111401-1.14677752227-0.636985393531-0.1134496566180.5191445689650.7920059226040.604881277795-0.112246421718-0.01600443413120.3896153537790.02022302397171.0444862482462.0304697742-5.18823300791-11.801591838
186.72505007259-1.351715572152.477621415641.222465453731.397959188625.16891220077-1.0662495585-0.8848174006132.00252889071-0.1463251978180.3977160812420.3941792104680.2744052878760.2323477526310.661711659880.704118892972-0.363889687930.07632095932870.3686431682460.2047301295440.53631033098168.19079510740.594801098234-6.51837614315
192.23203866024-1.64794537846-0.1043149300233.51870639396-0.4536059813480.007661254075170.245667370310.2224181120060.6048692725340.370662950845-0.1341851301130.452819175638-0.91055005567-0.001791285591240.4352003589620.703341468948-0.07808564490460.08990692411290.583257374963-0.02119649545560.12365381666751.41889808945.23310882119-5.97319681483
204.476541435570.123569479032-2.030279188864.520616018590.8719927531954.320508086360.6289209664980.04759608972491.33655514835-0.7614690759410.34465854474-0.506023546298-0.264846048954-0.166000938042-0.8066586984010.512573281005-0.085100706941-0.008911914041330.4716570889450.09016945133740.63798559633135.512692178811.7354698501-6.82343507227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 96 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 126 )
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 152 )
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 182 )
5X-RAY DIFFRACTION5chain 'A' and (resid 183 through 203 )
6X-RAY DIFFRACTION6chain 'D' and (resid 2 through 6 )
7X-RAY DIFFRACTION7chain 'D' and (resid 7 through 11 )
8X-RAY DIFFRACTION8chain 'D' and (resid 12 through 16 )
9X-RAY DIFFRACTION9chain 'D' and (resid 17 through 31 )
10X-RAY DIFFRACTION10chain 'D' and (resid 32 through 36 )
11X-RAY DIFFRACTION11chain 'D' and (resid 37 through 37 )
12X-RAY DIFFRACTION12chain 'B' and (resid 3 through 26 )
13X-RAY DIFFRACTION13chain 'B' and (resid 27 through 74 )
14X-RAY DIFFRACTION14chain 'B' and (resid 75 through 100 )
15X-RAY DIFFRACTION15chain 'B' and (resid 101 through 203 )
16X-RAY DIFFRACTION16chain 'A' and (resid 3 through 24 )
17X-RAY DIFFRACTION17chain 'A' and (resid 25 through 34 )
18X-RAY DIFFRACTION18chain 'A' and (resid 35 through 47 )
19X-RAY DIFFRACTION19chain 'A' and (resid 48 through 63 )
20X-RAY DIFFRACTION20chain 'A' and (resid 64 through 95 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more