[English] 日本語
Yorodumi
- PDB-7k1a: TtgR quadruple mutant (C137I I141W M167L F168Y) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7k1a
TitleTtgR quadruple mutant (C137I I141W M167L F168Y)
ComponentsHTH-type transcriptional regulator TtgR
KeywordsTRANSCRIPTION / TtgR / TetR family / epistasis
Function / homology
Function and homology information


DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding
Similarity search - Function
Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional regulator TtgR
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBingman, C.A. / Nishikawa, K.K. / Smith, R.W. / Raman, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM07215 United States
Department of Defense (DOD, United States)W911NF-17-1-0043 United States
CitationJournal: Nat Commun / Year: 2021
Title: Epistasis shapes the fitness landscape of an allosteric specificity switch.
Authors: Nishikawa, K.K. / Hoppe, N. / Smith, R. / Bingman, C. / Raman, S.
History
DepositionSep 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HTH-type transcriptional regulator TtgR
B: HTH-type transcriptional regulator TtgR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1664
Polymers48,1172
Non-polymers492
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-37 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.920, 64.280, 223.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein HTH-type transcriptional regulator TtgR / Toluene efflux pump ttgABC operon repressor


Mass: 24058.510 Da / Num. of mol.: 2 / Mutation: C137I, I141W, M167L, F168Y
Source method: isolated from a genetically manipulated source
Details: Quadruple mutant (C137I I141W M167L F168Y) / Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: DOT-T1E / Gene: ttgR, T1E_0244 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9AIU0
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 nL of protein at 9.7 mg/mL in 5mM HEPES pH 7.5, 50 mM NaCl, 0.3 mM TCEP was equilibrated against 150 nL 20% MEPEG, 0.2M MgCl2, 0.1M bistris HCl pH 6.5 in a SD2 plate using a Mosquito ...Details: 200 nL of protein at 9.7 mg/mL in 5mM HEPES pH 7.5, 50 mM NaCl, 0.3 mM TCEP was equilibrated against 150 nL 20% MEPEG, 0.2M MgCl2, 0.1M bistris HCl pH 6.5 in a SD2 plate using a Mosquito crystallization robot. Samples were cryoprotected with reservoir solution supplemented to 35% MEPEG 2000. Samples looped in Mitegen micro mounts were flash cooled by immersion in liquid nitrogen

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 16, 2018 / Details: 3.0G undulator, diamond (111)
RadiationMonochromator: diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→32.14 Å / Num. obs: 42585 / % possible obs: 99.71 % / Redundancy: 13.6 % / Biso Wilson estimate: 35.18 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.09432 / Rpim(I) all: 0.02647 / Rrim(I) all: 0.09805 / Net I/σ(I): 16.2
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.303 / Mean I/σ(I) obs: 1.29 / Num. unique obs: 4137 / CC1/2: 0.578 / CC star: 0.856 / Rpim(I) all: 0.4257 / Rrim(I) all: 1.373 / % possible all: 97.73

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UXU

2uxu


Resolution: 1.75→32.14 Å / SU ML: 0.2732 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1075
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2401 1979 4.65 %
Rwork0.1967 40587 -
obs0.1987 42566 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.41 Å2
Refinement stepCycle: LAST / Resolution: 1.75→32.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 2 279 3584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333375
X-RAY DIFFRACTIONf_angle_d0.47764570
X-RAY DIFFRACTIONf_chiral_restr0.0317519
X-RAY DIFFRACTIONf_plane_restr0.0022598
X-RAY DIFFRACTIONf_dihedral_angle_d20.35751268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.3885980.41522831X-RAY DIFFRACTION96.83
1.79-1.840.38061980.33932763X-RAY DIFFRACTION100
1.84-1.90.372990.27882961X-RAY DIFFRACTION100
1.9-1.960.27061980.2312794X-RAY DIFFRACTION100
1.96-2.030.2912990.21952888X-RAY DIFFRACTION99.97
2.03-2.110.2518990.21382919X-RAY DIFFRACTION100
2.11-2.20.24431980.19972857X-RAY DIFFRACTION100
2.2-2.320.242990.19242920X-RAY DIFFRACTION100
2.32-2.470.22241980.19152825X-RAY DIFFRACTION100
2.47-2.660.2502990.19772960X-RAY DIFFRACTION100
2.66-2.920.24061980.19472876X-RAY DIFFRACTION100
2.92-3.350.2464990.19772969X-RAY DIFFRACTION100
3.35-4.210.2311150.17912991X-RAY DIFFRACTION100
4.21-32.140.21831820.18213033X-RAY DIFFRACTION99.41
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)
12.412149144160.3496326109131.77759674863.232341559430.8822700522973.98388291115-0.000869527989615-0.04982663395910.05655029222950.2083516216570.13935455342-0.387898082224-0.01589641448920.3774180371037.66890687945E-50.3802823128060.0521535163698-0.0191781410640.333010675581-0.02703557114110.384866286426-13.0710614422-2.1928402504643.9120522526
22.21345385141-0.430903498819-0.2790906038350.998735404377-0.2474290164881.207287810120.0875779195328-0.00493789480176-0.0216220997980.07495725193920.0596265371152-0.113408803346-0.03107639162660.604334424972-2.33908318953E-50.3186030816970.00887434330546-0.02751186130510.370591878097-0.01445952470990.275274991269-17.5782818662-3.7078096654922.5394197094
32.97999531812-0.4747995395220.2537239518582.37348761849-0.6391631201710.75031028624-0.0937983506502-0.1429995813640.2171078338850.09102121421890.109030555033-0.0925291105622-0.5402489090390.8224357872320.0003383677568530.234051535508-0.0521923213659-0.0155526640940.2347294315310.01346100539940.295975604662-19.64288545728.8981076145619.679064759
42.74534150430.594322726924-0.2137431153051.56903431644-0.2684180308192.88828060592-0.07980774069460.28436734177-0.0956833515535-0.1614431145020.1775856767450.1783219924410.0975607005883-0.1466758040981.69185209402E-50.241713582963-0.00310648844386-0.02469431573730.216650074108-0.01368296117960.243852941063-28.7675538801-2.8830524191215.9030249077
50.5912858574040.200703068417-0.185672212351.471481488561.049633011871.442941105040.385539208663-0.07265657815290.536660671408-0.0048824671125-0.04886455577270.186998153203-0.15874483554-0.193735881806-9.1034430305E-70.3934768803140.06116497470540.06681310761390.3642304304510.05321612484290.358849446781-48.567368693311.739871865844.596786101
61.95813338481-0.62088930514-1.325852941440.521818072466-0.01305924124521.47169376610.312763534619-1.543813080060.4672425063580.4443232736660.108329544173-0.368254239819-0.822080060881.175525656910.05799765551740.3203988431180.05623200134140.02369018807880.363523120274-0.03623116509680.305461947604-38.9772962358.9576342880150.2017453532
70.7473677562691.02288306711-0.1987450623731.71605359564-0.3627218852411.16625715778-0.03933169875180.151353093346-0.148931273134-0.00413573443621-0.03576994890150.0395205597070.420005414119-0.707075338653-0.0008734900130160.3524044015490.03892869499090.03251680359290.3297048574640.04785495902450.403447302811-47.52429824793.7150773525946.4146698787
81.01874105483-0.1983205512980.4481579241091.383584350.3720752053181.136872749450.020396001946-0.1569562877450.1354551481620.181251192171-0.02963229935640.6841382233230.196284770455-0.615823388319-0.0009694697768250.29089302972-0.0410583733557-0.04240635913230.4216917762810.09589230389710.438759490867-49.5385582014.8684811583817.8637364458
90.3889087537360.4803697646280.3656712789770.8601529701390.07191860105310.7919260308840.124558613312-0.2094059880880.1176274409870.1091403939130.06655176447660.369348709799-0.315688899650.0480477535747-2.00213990936E-50.3199959012830.07018934668390.01167527554150.3137329686590.0004225469255250.387728203302-38.713310308110.254028769333.1043887219
101.42120203781-0.8938068559040.9431494401582.081275591990.2012845918541.13958961579-0.388308615246-1.93963706419-0.6241657214531.358998705920.6713567099241.333743991410.110874552267-1.404310331760.01341633657750.439222974747-0.008480861350820.04126900936160.5627774305720.1173639885060.58093815928-33.8731564453-3.1319789280142.2832280974
111.81414447920.04608725220090.04657031891662.395552748320.2667014847491.01114997566-0.0854319850342-0.178468518907-0.04269658523570.01897300357740.04818993007480.4522067252160.69331441338-0.350720464775-0.0003286369761220.303100954484-0.0602717963647-0.001907138985930.2456732902060.08134888408130.41155632099-44.3593344948-6.7264367313919.5311309558
121.22470401556-0.707645974686-0.6270196239290.959686757487-0.4813497909562.07164656545-0.06245895809040.0910667514247-0.01521969877960.3095515245550.2554901634410.1336570616830.271770051497-0.008527455261732.85438079148E-50.2782484804880.0562055042168-0.03225562673050.2767863683620.04653393979670.253677130033-34.77315734381.5693923569221.011324693
130.049960369587-0.04285912353110.1013466163070.0172773542472-0.06552922186050.129908114453-0.6940028384150.434908042250.665325827860.388630526956-0.1937962963710.244091129351-0.9668942056070.219198386167-0.000146552088710.387438126496-0.000530264212497-0.1247765226910.3368509244170.08508430979010.397726834345-32.022068774216.216679095619.9639281916
141.51579925468-0.761225665228-0.2083020084740.3602495964420.4174461212131.70488629276-0.1029354876040.3066368500760.0547769207052-0.3276044146850.2475141012560.0619560082770.07796175749-0.0917197822992-5.09011720252E-50.369937873683-0.0439620803485-0.04610122655720.3279034128990.07464267761440.269309236723-36.66757840881.719543025368.94211686163
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 68 )AA6 - 681 - 64
22chain 'A' and (resid 69 through 121 )AA69 - 12165 - 117
33chain 'A' and (resid 122 through 160 )AA122 - 160118 - 156
44chain 'A' and (resid 161 through 211 )AA161 - 211157 - 207
55chain 'B' and (resid 6 through 28 )BB6 - 282 - 24
66chain 'B' and (resid 29 through 42 )BB29 - 4225 - 38
77chain 'B' and (resid 43 through 67 )BB43 - 6739 - 63
88chain 'B' and (resid 68 through 103 )BB68 - 10364 - 99
99chain 'B' and (resid 104 through 116 )BB104 - 116100 - 112
1010chain 'B' and (resid 117 through 125 )BB117 - 125113 - 121
1111chain 'B' and (resid 126 through 160 )BB126 - 160122 - 156
1212chain 'B' and (resid 161 through 181 )BB161 - 181157 - 177
1313chain 'B' and (resid 182 through 191 )BB182 - 191178 - 187
1414chain 'B' and (resid 192 through 211 )BB192 - 211188 - 208

+
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