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- PDB-9llq: Structure of TetR2 and DNA probe -

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Basic information

Entry
Database: PDB / ID: 9llq
TitleStructure of TetR2 and DNA probe
Components
  • DNA (5'-D(P*AP*AP*AP*AP*AP*GP*AP*CP*TP*AP*AP*TP*CP*TP*GP*TP*CP*TP*AP*TP*CP*TP*AP*T)-3')
  • DNA (5'-D(P*AP*TP*AP*GP*AP*TP*AP*GP*AP*CP*AP*GP*AP*TP*TP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3')
  • TetR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / Transcriptional regulator / TetR
Function / homologyBacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / DNA binding / DNA / DNA (> 10) / TetR family transcriptional regulator
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHe, W. / Wen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No.82072237 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural and mechanistic insights into the transcriptional regulation of chromosomal T6SS by large conjugative plasmid-encoded TetRs in Acinetobacter baumannii.
Authors: He, W. / Ouyang, Z. / Zhang, J. / Guo, X. / Jiao, M. / Qin, Q. / He, X. / Kang, L. / Hwang, P.M. / Zheng, F. / Zhang, G. / Wen, Y.
History
DepositionJan 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR family transcriptional regulator
B: TetR family transcriptional regulator
E: DNA (5'-D(P*AP*AP*AP*AP*AP*GP*AP*CP*TP*AP*AP*TP*CP*TP*GP*TP*CP*TP*AP*TP*CP*TP*AP*T)-3')
F: DNA (5'-D(P*AP*TP*AP*GP*AP*TP*AP*GP*AP*CP*AP*GP*AP*TP*TP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)59,2974
Polymers59,2974
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-76 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.023, 116.521, 113.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

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Components

#1: Protein TetR family transcriptional regulator / TetR/AcrR family transcriptional regulator


Mass: 22281.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: AUO97_08420, EKS29_16065, F4T85_12235, FJU42_13590 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E3M4M0
#2: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*GP*AP*CP*TP*AP*AP*TP*CP*TP*GP*TP*CP*TP*AP*TP*CP*TP*AP*T)-3')


Mass: 7335.792 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli (E. coli)
#3: DNA chain DNA (5'-D(P*AP*TP*AP*GP*AP*TP*AP*GP*AP*CP*AP*GP*AP*TP*TP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3')


Mass: 7397.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium chloride,BIS-TRIS,PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 6, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→49.11 Å / Num. obs: 13225 / % possible obs: 98.68 % / Redundancy: 11.76 % / Biso Wilson estimate: 118.52 Å2 / CC1/2: 0.9992 / Net I/σ(I): 23.32
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 1251 / Rpim(I) all: 0.689

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPXdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8Z6E

8z6e


Resolution: 3.1→49.11 Å / SU ML: 0.5345 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.1931
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2693 1323 10 %
Rwork0.2231 11902 -
obs0.2278 13225 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 157.98 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 984 0 16 3903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224073
X-RAY DIFFRACTIONf_angle_d0.42515713
X-RAY DIFFRACTIONf_chiral_restr0.0283633
X-RAY DIFFRACTIONf_plane_restr0.0017551
X-RAY DIFFRACTIONf_dihedral_angle_d23.3941561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.220.41331300.38531241X-RAY DIFFRACTION93.84
3.22-3.370.39321430.33971282X-RAY DIFFRACTION97.67
3.37-3.550.34971440.30041313X-RAY DIFFRACTION99.12
3.55-3.770.37761540.2651314X-RAY DIFFRACTION98.99
3.77-4.060.27961480.24381322X-RAY DIFFRACTION99.46
4.06-4.470.25711400.22011335X-RAY DIFFRACTION99.53
4.47-5.110.27291540.19321325X-RAY DIFFRACTION99.86
5.12-6.440.27861450.24551357X-RAY DIFFRACTION99.87
6.45-49.110.21971650.18251413X-RAY DIFFRACTION99.68

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