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- PDB-9rtm: X-ray structure of the rhodamine-binding protein tag (Rho-tag) bo... -

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Basic information

Entry
Database: PDB / ID: 9rtm
TitleX-ray structure of the rhodamine-binding protein tag (Rho-tag) 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 / : / AraC effector-binding domain-containing protein
Function and homology information
Biological speciesChlorobaculum tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 rhodamine-binding protein tag (Rho-tag) 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:
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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)35,4684
Polymers34,6932
Non-polymers7752
Water48627
1
A: AraC effector-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7342
Polymers17,3471
Non-polymers3871
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)17,7342
Polymers17,3471
Non-polymers3871
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.090, 62.350, 96.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 17346.525 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M sodium phosphate citrate pH 4.2, 1.6 M sodium dihydrogen phosphate, 0.4 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: 1.00001 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 11, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.32
ReflectionResolution: 2.1→50 Å / Num. obs: 22503 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2884 / CC1/2: 0.905 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.7445
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2162 1132 5.03 %
Rwork0.1949 21371 -
obs0.22 22503 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.87 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 58 27 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852502
X-RAY DIFFRACTIONf_angle_d0.91323409
X-RAY DIFFRACTIONf_chiral_restr0.0457363
X-RAY DIFFRACTIONf_plane_restr0.006499
X-RAY DIFFRACTIONf_dihedral_angle_d18.1154938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.20.36561380.34972622X-RAY DIFFRACTION95
2.2-2.310.38931400.33242656X-RAY DIFFRACTION94.96
2.31-2.460.32261380.33372619X-RAY DIFFRACTION94.86
2.46-2.650.30951390.31462633X-RAY DIFFRACTION94.78
2.65-2.910.28441400.29022661X-RAY DIFFRACTION94.36
2.91-3.330.28381400.26312659X-RAY DIFFRACTION94.46
3.33-4.20.19481420.18762697X-RAY DIFFRACTION94.5
4.2-440.19371490.14642830X-RAY DIFFRACTION94.68

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