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- PDB-9r35: Crystal structure of the Pseudomonas putida Xre-RES toxin-antitox... -

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Basic information

Entry
Database: PDB / ID: 9r35
TitleCrystal structure of the Pseudomonas putida Xre-RES toxin-antitoxin complex bound to promoter DNA
Components
  • DNA forward (30-mer)
  • DNA reverse (30-mer)
  • Toxin Res
  • XRE anti-toxin
KeywordsGENE REGULATION / Protein-DNA complex / RES toxin / Xre antitoxin
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / DNA binding
Similarity search - Function
Antitoxin Xre / Antitoxin Xre-like, helix-turn-helix domain / Antitoxin Xre-like helix-turn-helix domain / Antitoxin Xre/MbcA/ParS-like, toxin-binding domain / Antitoxin Xre/MbcA/ParS C-terminal toxin-binding domain / RES domain / RES domain / RES
Similarity search - Domain/homology
DNA / DNA (> 10) / Antitoxin / Toxin Res
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHenriksen, F.O.G. / Brodersen, D.E.
Funding support Denmark, 3items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0030646 Denmark
Novo Nordisk FoundationNNF22OC0079855 Denmark
Independent Research Fund Denmark - Medical Sciences0135-00072B Denmark
CitationJournal: Plos Genet. / Year: 2025
Title: Structural basis for higher-order DNA binding by a bacterial transcriptional regulator.
Authors: Henriksen, F.O.G. / Van, L.B. / Brodersen, D.E. / Skjerning, R.
History
DepositionMay 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin Res
B: XRE anti-toxin
C: XRE anti-toxin
D: Toxin Res
E: XRE anti-toxin
F: XRE anti-toxin
G: Toxin Res
H: XRE anti-toxin
I: XRE anti-toxin
J: Toxin Res
K: XRE anti-toxin
L: XRE anti-toxin
M: Toxin Res
N: XRE anti-toxin
O: XRE anti-toxin
P: Toxin Res
Q: XRE anti-toxin
R: XRE anti-toxin
S: Toxin Res
T: XRE anti-toxin
U: XRE anti-toxin
V: Toxin Res
W: XRE anti-toxin
X: XRE anti-toxin
a: DNA reverse (30-mer)
b: DNA forward (30-mer)
c: DNA forward (30-mer)
d: DNA reverse (30-mer)
e: DNA forward (30-mer)
f: DNA reverse (30-mer)
g: DNA forward (30-mer)
h: DNA reverse (30-mer)


Theoretical massNumber of molelcules
Total (without water)485,63332
Polymers485,63332
Non-polymers00
Water1,17165
1
A: Toxin Res
B: XRE anti-toxin
C: XRE anti-toxin
D: Toxin Res
E: XRE anti-toxin
F: XRE anti-toxin
a: DNA reverse (30-mer)
b: DNA forward (30-mer)


Theoretical massNumber of molelcules
Total (without water)121,4088
Polymers121,4088
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17680 Å2
ΔGint-81 kcal/mol
Surface area42680 Å2
2
G: Toxin Res
H: XRE anti-toxin
I: XRE anti-toxin
J: Toxin Res
K: XRE anti-toxin
L: XRE anti-toxin
c: DNA forward (30-mer)
d: DNA reverse (30-mer)


Theoretical massNumber of molelcules
Total (without water)121,4088
Polymers121,4088
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18050 Å2
ΔGint-88 kcal/mol
Surface area42790 Å2
3
M: Toxin Res
N: XRE anti-toxin
O: XRE anti-toxin
P: Toxin Res
Q: XRE anti-toxin
R: XRE anti-toxin
e: DNA forward (30-mer)
f: DNA reverse (30-mer)


Theoretical massNumber of molelcules
Total (without water)121,4088
Polymers121,4088
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18180 Å2
ΔGint-88 kcal/mol
Surface area43720 Å2
4
S: Toxin Res
T: XRE anti-toxin
U: XRE anti-toxin
V: Toxin Res
W: XRE anti-toxin
X: XRE anti-toxin
g: DNA forward (30-mer)
h: DNA reverse (30-mer)


Theoretical massNumber of molelcules
Total (without water)121,4088
Polymers121,4088
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18200 Å2
ΔGint-74 kcal/mol
Surface area42700 Å2
Unit cell
Length a, b, c (Å)81.23, 185.11, 170.79
Angle α, β, γ (deg.)90, 90.01, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Toxin Res


Mass: 17523.775 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: N-terminally hexa His-tagged / Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: res, PP_2434 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q88K57, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Protein
XRE anti-toxin


Mass: 16978.436 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: AYO08_12380, B7H19_10555, CBL13_00496, CBP06_13110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A179RFM7
#3: DNA chain
DNA reverse (30-mer)


Mass: 9180.899 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida KT2440 (bacteria)
#4: DNA chain
DNA forward (30-mer)


Mass: 9265.994 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Pseudomonas putida KT2440 (bacteria)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.48 %
Description: Triagonal plate-shaped crystals of 0.2-0.4 micrometer in diagonal length
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Na-HEPES, pH 7.5, 10% (w/v) PEG 8000, 8% (v/v) ethylenglycol, and 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2024
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.6→26.03 Å / Num. obs: 139781 / % possible obs: 90.3 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.108 / Net I/σ(I): 8.13
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.6-2.671.39363090.2891.6871
2.67-2.741.18770580.3771.4251
2.74-2.820.98578480.4341.1791
2.82-2.910.81887130.5770.9751
2.91-30.704100470.6870.8371
3-3.110.57897810.8040.681
3.11-3.220.42494350.8790.4981
3.22-3.360.28690480.9440.3371
3.36-3.510.19887190.970.2331
3.51-3.680.14583960.9810.1711
3.68-3.880.11179370.9870.1311
3.88-4.110.09175300.9910.1081
4.11-4.390.07570370.9930.0891
4.39-4.750.06365880.9940.0741
4.75-5.20.06260280.9940.0731
5.2-5.810.05954790.9940.071
5.81-6.710.05548730.9950.0661
6.71-8.220.04741050.9960.0561
8.22-11.630.04131760.9960.0491
11.63-26.030.0416740.9960.0471

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Processing

Software
NameVersionClassification
PHENIX2.8.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→26.03 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.269 6987 5 %Random selection
Rwork0.228 ---
obs-132754 90.3 %-
Refinement stepCycle: LAST / Resolution: 2.7→26.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27971 3481 0 65 31517

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