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- PDB-8v90: TtgR variant 3A7 with naltrexone -

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Basic information

Entry
Database: PDB / ID: 8v90
TitleTtgR variant 3A7 with naltrexone
ComponentsHTH-type transcriptional regulator TtgR
KeywordsTRANSCRIPTION / regulatory / TetR like
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 DOT-T1E (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsAcheson, J.F. / Lee, D. / Ramen, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W911NF-20-C0005 United States
CitationJournal: To Be Published
Title: TtgR variant 3A7 with naltrexone
Authors: Acheson, J.F. / Lee, D. / Ramen, S.
History
DepositionDec 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 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: HTH-type transcriptional regulator TtgR
B: HTH-type transcriptional regulator TtgR
C: HTH-type transcriptional regulator TtgR
D: HTH-type transcriptional regulator TtgR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,62114
Polymers96,4754
Non-polymers2,14610
Water3,819212
1
A: HTH-type transcriptional regulator TtgR
B: HTH-type transcriptional regulator TtgR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6528
Polymers48,2372
Non-polymers1,4146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-35 kcal/mol
Surface area17980 Å2
MethodPISA
2
C: HTH-type transcriptional regulator TtgR
D: HTH-type transcriptional regulator TtgR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9696
Polymers48,2372
Non-polymers7314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-38 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.100, 43.169, 115.826
Angle α, β, γ (deg.)99.070, 97.020, 95.970
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


Mass: 24118.732 Da / Num. of mol.: 4 / Mutation: A75L, L94W, N111M, H115F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida DOT-T1E (bacteria) / Gene: ttgR / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9AIU0
#2: Chemical
ChemComp-YOE / nalterxone


Mass: 341.401 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H23NO4 / 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.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris pH 6.5 18- 20% MEPEG 2000, 200 mM MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 31, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.08→27.6 Å / Num. obs: 44735 / % possible obs: 91.56 % / Redundancy: 3.5 % / Biso Wilson estimate: 38.14 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.048 / Net I/σ(I): 9.34
Reflection shellResolution: 2.08→2.154 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 4030 / CC1/2: 0.894 / % possible all: 81.13

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→27.6 Å / SU ML: 0.2328 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.9046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2492 1799 4.03 %
Rwork0.2012 42878 -
obs0.2031 44677 91.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.38 Å2
Refinement stepCycle: LAST / Resolution: 2.08→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6619 0 154 212 6985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00276928
X-RAY DIFFRACTIONf_angle_d0.81599421
X-RAY DIFFRACTIONf_chiral_restr0.03231060
X-RAY DIFFRACTIONf_plane_restr0.00471198
X-RAY DIFFRACTIONf_dihedral_angle_d13.75251012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.140.29611190.25312865X-RAY DIFFRACTION78.32
2.14-2.20.32861310.25343250X-RAY DIFFRACTION91.18
2.2-2.270.30411490.24513415X-RAY DIFFRACTION93.99
2.27-2.350.27851460.23283278X-RAY DIFFRACTION92.82
2.35-2.450.29711380.23363363X-RAY DIFFRACTION93.36
2.45-2.560.27781420.22363344X-RAY DIFFRACTION91.69
2.56-2.690.30961350.22453132X-RAY DIFFRACTION87.12
2.69-2.860.25141380.22243419X-RAY DIFFRACTION95.03
2.86-3.080.23271470.24143414X-RAY DIFFRACTION94.91
3.08-3.390.27281430.22643364X-RAY DIFFRACTION94.05
3.39-3.880.26241270.18773224X-RAY DIFFRACTION89.07
3.88-4.880.20691450.1643441X-RAY DIFFRACTION95.88
4.88-27.60.21291390.17213369X-RAY DIFFRACTION93.77
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)
14.219951177971.46097578009-1.184375963768.40762894114-1.55218356656.069313603210.0266943800101-0.3173966507370.09128455246490.251965294448-0.07241082869860.2704742414210.165725821434-0.3765154351340.05420809135110.2559980006450.000826259165655-0.02520429452370.409803783473-0.03306660772960.230136782189-12.2227722239-11.3621869672-11.5893299967
24.57456341163-4.53425051655-5.098203860868.310197709616.283936622569.78164240582-0.3585068317210.21256237143-0.8229358871490.0831961899928-0.1010887392210.6356401096030.639053557437-0.1466935245590.5194694854120.323866717802-0.0639463201811-0.04332274251950.553127730371-0.04120096650650.361370435496-12.6216263063-9.49664676122-39.9795762493
31.81604540653-0.1692639547260.3964149048341.78770038980.5847030564424.69165721468-0.02893266200080.1923574128660.000269704750471-0.2574555492230.02831737880520.0856440329533-0.0611918923726-0.01231973399970.0286352241090.285921205184-0.0857603681195-0.01966482781370.380367700507-0.001965139693050.285010125054-1.8963340401-4.94381222262-35.5288774373
46.36632124095.008072062583.04680907999.177272606042.650931163645.123394886720.0848769029627-0.134159534299-0.405015386610.302691053749-0.0434682638409-0.6173459674030.1383790612780.283598649787-0.01920301719620.2827900245280.0257216469546-0.03688430609980.442281960698-0.06673828377180.2438454136319.44420380634.5977253221-9.41698296865
53.25882529920.1421700794121.539260251611.9797121544-1.371944999853.50996680359-0.3097022848420.4225594731820.505893388432-0.4506190679030.375959523982-0.172045652651-0.2539228265010.2796159906480.02099330041050.429467814386-0.106658085380.001512211062340.423679324437-0.06328389007260.3999688868816.306486802111.8166538639-17.9816448135
62.003681860170.350608600312-0.4423848586821.970233716620.2614702362282.91579202414-0.0557701369580.1779696326910.268789179421-0.245427095160.104345408175-0.0510641049848-0.3301977197850.150021591738-0.05380117166180.296920138075-0.0771108437964-0.01350996306430.3448761945180.002528128657410.284355317438.877478996125.97596903383-35.6795593858
78.153302222831.98225072101-2.481157695917.69474947045-1.911307134855.22263916861-0.06781502300190.3157554678720.282636541974-0.5187842363840.0595664369989-0.0945909865927-0.175156930340.208303143488-0.08527211164780.429723852437-0.00246433757753-0.03114357578360.2699108132010.03677969865980.2347402994368.5867325450913.13147125579.78476191145
80.852295672563-0.2248368799831.014830698470.256639940311-0.8239283388299.41934180259-0.0834787007226-0.1982972352060.08099590674980.302396614106-0.00613590141984-0.312953234491-0.1407658794030.6336132488580.1210456090610.550111276072-0.0487051014262-0.04438652171870.360046873182-0.02225728015110.3276767208597.9101941150811.253145429135.1500770089
95.86128189211-3.33966970782-1.612209312133.687010296134.491356100977.986141919520.09466817360570.1062697742290.158957556922-0.3304043355850.205932970772-0.499180140583-0.3900277215840.013996674853-0.2158715749810.360950436006-0.0523442786494-0.006394919541810.2548370432380.02893045461540.2545182698442.743131329563.0459053973320.0417458251
102.56481086786-0.6805048025870.2331268045163.413299266042.22222520965.647095307270.265310627778-0.1733565250360.01227342202420.3554566528150.152275373977-0.345417989555-0.2191960173380.446707723217-0.3295740362390.317325463793-0.0632752925804-0.05965932323470.2871184753560.02636590260280.27700944580512.77537398090.70378027297639.457801398
115.87155842008-1.610973334093.358311860743.75609469472-0.5322045833956.60488783720.161002150499-0.370407243-0.01886209901680.09177940865580.02370717245880.2361840330130.0967872607067-0.341202041047-0.2236016766320.361850629214-0.0689964780537-0.01335297607260.2730693411640.01077293126130.274593390572-1.954281617690.86122410264940.4553534927
127.399917222643.172970350270.3745915264738.434778383962.700850893954.304475119130.1347209367950.0283483484728-0.240856154907-0.0717707633163-0.04698066573650.1129027047520.128798228619-0.0973870972443-0.05887586719450.391001426160.0189752819147-0.09809125601560.2727622869430.01388085201990.235461769461-6.10578610991-19.99941898249.63978946921
133.97408141472-1.92927377762-5.709761960862.876836840341.781378980919.30078851009-0.08378817125770.417034834009-0.9846461467190.0671147058863-0.05488398033520.7439543608520.554656701147-0.963011063240.1430888064620.520301668534-0.0697146309604-0.0859367449830.424147289640.04807479728740.668034334023-9.94039725727-19.783478429938.4240189104
142.4652168506-0.114111815337-0.1499664073141.49724925462-0.1089758581162.625455877630.0485855806177-0.250058557416-0.2296722629620.0144322030757-0.00969907031850.2155788257970.0964483228984-0.251268065633-0.03404569373060.419753082902-0.067603447848-0.05282835992310.3253334797930.03820032319930.357295116117-5.61169322606-8.7067486528334.7377525487
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 66 )AA5 - 661 - 62
22chain 'A' and (resid 67 through 102 )AA67 - 10263 - 98
33chain 'A' and (resid 103 through 210 )AA103 - 21099 - 206
44chain 'B' and (resid 4 through 41 )BD4 - 411 - 38
55chain 'B' and (resid 42 through 78 )BD42 - 7839 - 75
66chain 'B' and (resid 79 through 210 )BD79 - 21076 - 207
77chain 'C' and (resid 5 through 54 )CG5 - 541 - 50
88chain 'C' and (resid 55 through 102 )CG55 - 10251 - 98
99chain 'C' and (resid 103 through 124 )CG103 - 12499 - 120
1010chain 'C' and (resid 125 through 159 )CG125 - 159121 - 155
1111chain 'C' and (resid 160 through 210 )CG160 - 210156 - 206
1212chain 'D' and (resid 3 through 66 )DH3 - 661 - 64
1313chain 'D' and (resid 67 through 102 )DH67 - 10265 - 100
1414chain 'D' and (resid 103 through 210 )DH103 - 210101 - 208

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