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- PDB-7kd8: TtgR C137I I141W M167L F168Y mutant in complex with resveratrol -

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Basic information

Entry
Database: PDB / ID: 7kd8
TitleTtgR C137I I141W M167L F168Y mutant in complex with resveratrol
ComponentsHTH-type transcriptional regulator TtgR
KeywordsTRANSCRIPTION / TtgR / TetR family / epistasis / resveratrol
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
RESVERATROL / HTH-type transcriptional regulator TtgR
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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
DepositionOct 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,24412
Polymers96,2344
Non-polymers1,0108
Water5,945330
1
A: HTH-type transcriptional regulator TtgR
B: HTH-type transcriptional regulator TtgR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6226
Polymers48,1172
Non-polymers5054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-33 kcal/mol
Surface area18760 Å2
MethodPISA
2
D: HTH-type transcriptional regulator TtgR
C: HTH-type transcriptional regulator TtgR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6226
Polymers48,1172
Non-polymers5054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-30 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.497, 43.587, 115.942
Angle α, β, γ (deg.)97.969, 98.648, 96.761
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 24058.510 Da / Num. of mol.: 4 / Mutation: C137I I141W M167L F168Y
Source method: isolated from a genetically manipulated source
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-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein at 10.4 mg/ml (433 uM) incubated 30 min with 1 mM resveratrol dissolved in ethanol. 2 microliters of protein was mixed with 2 microliters of reservoir consisting of 12% MEPEG 2000, ...Details: Protein at 10.4 mg/ml (433 uM) incubated 30 min with 1 mM resveratrol dissolved in ethanol. 2 microliters of protein was mixed with 2 microliters of reservoir consisting of 12% MEPEG 2000, 5% MPD, 0.3 M MGCL2, 100 MM BISTRIS pH 6.5. The droplet was set on a siliconized glass cover slip to minimize loss of resveratrol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07812 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: May 30, 2019
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 1.71→25.65 Å / Num. obs: 82430 / % possible obs: 91.78 % / Redundancy: 3.8 % / Biso Wilson estimate: 31.21 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.04573 / Rpim(I) all: 0.02758 / Rrim(I) all: 0.05349 / Net I/σ(I): 13.88
Reflection shellResolution: 1.71→1.771 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.5776 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 8133 / CC1/2: 0.901 / CC star: 0.974 / Rrim(I) all: 0.6697 / % possible all: 91.33

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
XDS20200417data reduction
XDS20200417data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7K1A

7k1a


Resolution: 1.71→25.65 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.6686
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 1984 2.41 %thin shell
Rwork0.1932 80326 --
obs0.1943 81923 91.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.02 Å2
Refinement stepCycle: LAST / Resolution: 1.71→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 72 330 7052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00537029
X-RAY DIFFRACTIONf_angle_d0.71099518
X-RAY DIFFRACTIONf_chiral_restr0.04071062
X-RAY DIFFRACTIONf_plane_restr0.00391251
X-RAY DIFFRACTIONf_dihedral_angle_d17.05842642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.41921360.33785591X-RAY DIFFRACTION88.37
1.75-1.80.30811450.30735732X-RAY DIFFRACTION92.93
1.8-1.850.33011430.2545800X-RAY DIFFRACTION92.58
1.85-1.910.28551400.22815775X-RAY DIFFRACTION92
1.91-1.980.23471470.2115823X-RAY DIFFRACTION92.36
1.98-2.060.30071420.22075754X-RAY DIFFRACTION92.54
2.06-2.150.25511390.20095707X-RAY DIFFRACTION91.03
2.15-2.260.23641390.19375440X-RAY DIFFRACTION86.85
2.26-2.40.23191400.19485547X-RAY DIFFRACTION88.46
2.4-2.590.24161480.19665913X-RAY DIFFRACTION95.19
2.59-2.850.2551410.19985941X-RAY DIFFRACTION94.87
2.85-3.260.25071400.20465871X-RAY DIFFRACTION93.98
3.26-4.110.22391410.17755597X-RAY DIFFRACTION89.22
4.11-28.110.21841430.16915835X-RAY DIFFRACTION93.04
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)
11.43150303868-0.587643333652-0.2850368120421.20372389661-0.3853366851811.59238621291-0.3009314368710.3053982510880.369096009832-0.605387769270.385213088202-0.114797297397-0.4864234341010.220183893740.009615041192010.3975627638190.002269800065570.02683596712760.2944895618840.03258894437990.373595579242-9.7087859037-8.47924556965-45.8610960036
20.346843477222-0.0375901214962-0.3279676021630.821735874301-0.1899592356320.8900305528620.407145153219-0.3034790745040.288087328640.318138347432-0.161046104685-0.240250663551-0.723643977280.6784456850920.01463228301720.497490418742-0.08179415386570.01651376607620.365638254608-0.0401667468970.367375969767-10.9999017368-10.0776592904-20.2107511803
32.063644124840.734432445284-0.4007689886782.22319856209-0.1895274687172.871775291010.255371915305-0.2533188294040.04100452244880.244059880581-0.191262441418-0.06482846848-0.1607274620350.1895988219180.001953855147660.2069449225940.022408032804-0.009623654091220.194526992766-0.005213562102770.231574675442-14.3006686687-20.9370291261-21.6990137611
40.903070177153-0.7028689769520.2363700402190.7091039852380.05290959442980.7586950721850.119091892727-0.0336753196968-0.4719028427790.0442883546156-0.00295309032613-0.3903033915380.308275071517-0.1059632103790.0001018191321240.3389203312590.0387338907344-0.01642072352310.283172901029-0.008308857119070.346174650956-23.2245327566-45.6838778708-44.3989944825
50.875118766568-0.3402807060770.675027521910.836457612230.02499515861150.8585828306830.06038623195110.03884206352780.116024104275-0.183903030239-0.04611638861810.103457765875-0.12175249662-0.05946874175672.39497083201E-70.3656635442090.00299090462899-0.02775904475530.287947850834-0.005492497358350.356768443357-25.1364708666-38.4088095975-46.6895087287
60.3995431699280.201077999006-0.3029692800820.3943487792490.1235202494721.219396329160.403774882190.221378757601-0.4822403796790.331283741062-0.2923382490890.1400274029610.675834355309-1.037076828420.02281990702760.536253053507-0.1514943135660.004903523889260.4327196897760.007868537237740.398764863546-28.0669772859-41.7786508048-17.9204039941
70.7304921481120.475847886526-0.2864820394590.6813141150510.2293672286580.588580337953-0.1332165044270.356068832774-0.0238998312537-0.2197852133940.1328043320740.2430442414910.0215625491357-0.1653123581411.01084011344E-70.3250808391210.0322756331394-0.03315509449210.3178386055910.01433929112540.359260917791-20.5559064788-31.1405671645-37.13185026
80.712248552328-0.4784355932430.3553042469350.9668322811820.1689697866780.5227762732040.198810549044-0.190933087650.1195491022390.282035276489-0.2204180126410.4099612603890.363146954575-1.27079626775-0.02811328305690.329236209559-0.1109886186340.06365031073710.504890005174-0.02546972699320.334304142358-33.6963493622-29.9268643738-18.3074650792
90.3587108786780.2682033348560.387537631790.620584116569-0.250678236371.114907263840.276475503396-0.215674032611-0.1186937254030.2898993628-0.2106936738950.02045896650520.0782823334994-0.1668029965260.004013230920550.2372760513470.053989673767-0.03005898660150.1559070395590.02999523091930.285277409287-19.4958700202-28.2955440688-21.2666285307
101.013750337840.8141075050810.62782870851.43437684947-0.3902214841581.327020869480.342000453439-0.543507376306-0.1750738109890.513502360446-0.319311711746-0.09054113393550.226471240004-0.150625135857-1.95281581791E-70.440975378312-0.0754294417411-0.03957759024290.3854250220170.04154430705890.31558427151-18.3805797006-31.689430657-11.6417462435
110.676841282797-0.8135751641620.111017823381.41792296780.03591305263520.930920574610.311495387353-0.304717539480.2653290662440.253606033027-0.2000289947610.8845996738790.226959185781-0.459241766860.006901922589110.2850969095870.03478474681760.02237527233670.4388354456470.02198635790010.430339448145-14.2319275496-7.0878456100344.5907364159
120.447631571328-0.06799192249040.3581814245570.518063652136-0.4496314729860.5750468707270.454778694891-0.797049548849-0.2259152173870.842002305093-0.4956722325350.0173598054101-0.004674026226370.0459558814385-0.004538020490550.342674092725-0.04574808722320.02204949406870.4189151240250.0423206101150.337261064207-7.64247936485-9.113622768151.033861176
130.3758511008360.1488995887120.07335990820980.334392567575-0.1792596489960.175475445458-0.08342346196820.503823664893-0.251307264874-0.5464711386430.138796325407-0.354827150080.9249388330240.430912438402-0.003186848789970.3492129144520.0417234360019-0.01618766570750.3296408638650.01131603148040.34968164451-5.77948096641-9.2593480871535.9986692189
141.00849872233-0.241563698441-0.07649435727910.774490651919-0.4631594214430.69888158021-0.5128172582390.610684522829-0.283089651841-0.6313394521590.5099143279880.6533580895960.933472144055-0.6617569660610.03183726908490.479461805941-0.193375213829-0.04356609964870.554500092731-0.00559078095630.367097633908-10.5285014361-5.7855845123217.6829755331
150.4748882962730.299930776978-0.1398069098620.5743297233980.3593178951790.7538354488260.125205598125-0.0928955063833-0.2716876773040.3636063394580.0953241280621-0.06621716810050.145781508476-0.0992739464514-8.04704111079E-70.2811781064710.0748395817299-0.05492439084550.3077181147770.01076861842870.3678704027491.47218760889-3.5723415763139.4356142475
160.755441913845-0.531054309121-0.02203396232430.4931487173970.1371812447840.695443569479-0.6499608243240.493523542569-0.97284100579-0.8660627305020.600326320408-0.2483972296340.8469499324080.147670195021-0.1445796031170.675522637249-0.2873652745940.06993663941470.471746872015-0.1787903493520.3199101423621.97375853896-10.409466593717.5735821349
170.8687104718970.6317836058420.1102030283010.652460970021-0.3266233011440.841501533792-0.4555644671340.380812353932-0.0818759144611-0.328137108830.524538112151-0.1071497900370.194936832659-0.0005455615914570.02264239184550.2229087885250.00398083776015-0.004282259956590.2902593633480.01031155755320.2356311651762.133048703733.0692422693823.0694463757
180.2554072300950.126360076722-0.04712019599410.0650381464434-0.01913371966180.176793137713-0.2483812649990.1772236077490.5652506817540.007438400282640.2454258367640.626892660683-0.352046358177-0.1147741286960.01484277654110.497802353637-0.0172537077188-0.1213985540880.4958046479050.1695489291410.458589751506-7.298814111113.205813312322.8069341148
190.4122860327180.804714058997-0.009565275775292.072276837860.2660756110.198932685918-0.4856267760171.009179349770.160264798157-1.394029484110.876507361729-0.1602978736930.0309252683292-0.3075898640210.1378781617080.611860879881-0.255995544038-0.03166163545050.5889965900790.04142192422630.1537761993842.136359261092.19708464259.92250328247
201.44072961915-0.4970492174490.2912046230680.8536100988850.04753265467371.73376736120.129984583312-0.132861161715-0.09433953708080.171726536684-0.0695546076518-0.1549959617410.01460116135910.06572817584935.03062558065E-80.2389067150520.0446162973516-0.01597816041280.300511540168-0.02181466055990.32296321191420.50723897879.0248307925349.590688981
210.3521775435750.65386201050.2560778104880.4582069568840.2667577503140.952630080815-0.1116633401770.1632492308540.136092808365-0.2048211901250.362211722079-0.214145115615-0.9415800711380.6374566131590.01111027866040.446547107604-0.08928675282730.03389617398740.475363090797-0.02506498104780.40894334222919.242474899613.798013565824.1198865303
222.490612367141.20007050634-0.115539554832.80812309008-0.2669894135422.821858041-0.2789488375190.3184643450330.0865369525395-0.315343108220.296931452676-0.111385696525-0.2141574687090.04600163543790.002078672316350.248166438526-0.03472619483270.02079455826730.267181309243-0.01288191227440.2452175162779.387153643528.6409422349723.197671969
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 55 )AA5 - 552 - 53
22chain 'A' and (resid 56 through 103 )AA56 - 10354 - 101
33chain 'A' and (resid 104 through 211 )AA104 - 210102 - 216
44chain 'B' and (resid 4 through 28 )BF4 - 282 - 26
55chain 'B' and (resid 29 through 67 )BF29 - 6727 - 65
66chain 'B' and (resid 68 through 103 )BF68 - 10366 - 102
77chain 'B' and (resid 104 through 125 )BF104 - 125103 - 124
88chain 'B' and (resid 126 through 160 )BF126 - 160125 - 159
99chain 'B' and (resid 161 through 181 )BF161 - 181160 - 181
1010chain 'B' and (resid 182 through 211 )BF182 - 210182 - 211
1111chain 'C' and (resid 4 through 28 )CH4 - 281 - 26
1212chain 'C' and (resid 29 through 55 )CH29 - 5527 - 53
1313chain 'C' and (resid 56 through 67 )CH56 - 6754 - 65
1414chain 'C' and (resid 68 through 103 )CH68 - 10366 - 101
1515chain 'C' and (resid 104 through 125 )CH104 - 125102 - 130
1616chain 'C' and (resid 126 through 160 )CH126 - 160131 - 165
1717chain 'C' and (resid 161 through 181 )CH161 - 181166 - 187
1818chain 'C' and (resid 182 through 191 )CH182 - 191188 - 198
1919chain 'C' and (resid 192 through 211 )CH192 - 210199 - 217
2020chain 'D' and (resid 6 through 55 )DG6 - 554 - 53
2121chain 'D' and (resid 56 through 103 )DG56 - 10354 - 101
2222chain 'D' and (resid 104 through 211 )DG104 - 210102 - 208

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  • 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

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