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- PDB-9rtl: X-ray structure of the CTR107-N138A mutant bound to a tetramethyl... -

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Basic information

Entry
Database: PDB / ID: 9rtl
TitleX-ray structure of the CTR107-N138A mutant bound to a tetramethylrhodamine ligand
ComponentsAraC effector-binding domain-containing protein
KeywordsUNKNOWN FUNCTION / Rhodamine-binding protein / Rho-tag / Tetramethylrhodamine
Function / homologyBacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / GyrI-like small molecule binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / : / Bacterial transcription activator effector binding domain-containing protein
Function and homology information
Biological speciesChlorobaculum tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTarnawski, M. / Kompa, J. / Johnsson, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: X-ray structure of the CTR107-N138A mutant bound to a tetramethylrhodamine ligand
Authors: Tarnawski, M. / Kompa, J. / Johnsson, K.
History
DepositionJul 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AraC effector-binding domain-containing protein
B: AraC effector-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8249
Polymers34,5892
Non-polymers1,2357
Water2,216123
1
A: AraC effector-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0506
Polymers17,2941
Non-polymers7565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AraC effector-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7743
Polymers17,2941
Non-polymers4802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.810, 71.810, 146.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein AraC effector-binding domain-containing protein


Mass: 17294.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum TLS (bacteria) / Gene: CT0179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KFZ1
#2: Chemical ChemComp-A1EI4 / [9-(2-carboxyphenyl)-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium / 9-(2-carboxyphenyl)-3,6-bis(dimethylamino)xanthylium


Mass: 387.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium acetate pH 4.5, 0.88 M sodium dihydrogen phosphate and 1.32 M potassium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 22, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 39388 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 32.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.041 / Net I/σ(I): 29.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 6 / Num. unique obs: 5878 / CC1/2: 0.97 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.35 Å / SU ML: 0.2205 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.3608
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2133 1970 5 %
Rwork0.1825 37416 -
obs0.184 39386 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 88 123 2554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332490
X-RAY DIFFRACTIONf_angle_d1.33663379
X-RAY DIFFRACTIONf_chiral_restr0.0815353
X-RAY DIFFRACTIONf_plane_restr0.0096494
X-RAY DIFFRACTIONf_dihedral_angle_d17.9065924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.33031410.27022680X-RAY DIFFRACTION99.86
1.85-1.890.29631400.22782647X-RAY DIFFRACTION99.96
1.89-1.950.26261400.2012659X-RAY DIFFRACTION99.96
1.95-2.010.25241400.2092661X-RAY DIFFRACTION100
2.01-2.090.2611410.21672679X-RAY DIFFRACTION99.93
2.09-2.170.27661390.19862659X-RAY DIFFRACTION100
2.17-2.270.23021410.1982668X-RAY DIFFRACTION99.93
2.27-2.390.22271410.20262682X-RAY DIFFRACTION99.96
2.39-2.540.25131400.20392664X-RAY DIFFRACTION99.93
2.54-2.730.25221400.20962658X-RAY DIFFRACTION99.93
2.73-3.010.2751420.21482700X-RAY DIFFRACTION99.96
3.01-3.440.20721410.19482669X-RAY DIFFRACTION99.96
3.44-4.330.18811400.15332672X-RAY DIFFRACTION99.93
4.34-38.350.14261440.14422718X-RAY DIFFRACTION99.9

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