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- PDB-8z6d: Structure of transcriptional regulator TetR1 -

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Basic information

Entry
Database: PDB / ID: 8z6d
TitleStructure of transcriptional regulator TetR1
ComponentsTetR/AcrR family transcriptional regulator
KeywordsDNA BINDING PROTEIN / transcriptional regulator / TetR
Function / homology: / 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 / DNA binding / TetR/AcrR family transcriptional regulator
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHe, W. / Wen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)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
DepositionApr 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR/AcrR family transcriptional regulator
C: TetR/AcrR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)43,9732
Polymers43,9732
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-31 kcal/mol
Surface area15880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.170, 69.360, 112.440
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 TetR/AcrR family transcriptional regulator / transcriptional regulator TetR1


Mass: 21986.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: F4T85_12205, FJU42_20375, HBK86_20415 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A1SW14
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium acetate, BIS-TRIS pH 5.5, 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: Sep 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→46.57 Å / Num. obs: 23865 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.081 / Net I/σ(I): 16.61
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.39 / Num. unique obs: 2366 / CC1/2: 0.684

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.1→46.57 Å / SU ML: 0.2486 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 25.8461
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2506 1989 9.59 %
Rwork0.2018 18759 -
obs0.2065 20748 86.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2807 0 0 179 2986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00762855
X-RAY DIFFRACTIONf_angle_d0.79273856
X-RAY DIFFRACTIONf_chiral_restr0.0468454
X-RAY DIFFRACTIONf_plane_restr0.0048481
X-RAY DIFFRACTIONf_dihedral_angle_d4.5486368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.2917500.273473X-RAY DIFFRACTION31.24
2.16-2.210.2823920.2676872X-RAY DIFFRACTION57.01
2.21-2.280.5376500.4248457X-RAY DIFFRACTION30.73
2.28-2.350.29221490.24281408X-RAY DIFFRACTION91.8
2.35-2.440.25661630.22651529X-RAY DIFFRACTION99.94
2.44-2.530.27091620.22251531X-RAY DIFFRACTION99.94
2.53-2.650.27081610.22031522X-RAY DIFFRACTION100
2.65-2.790.29051630.23271535X-RAY DIFFRACTION99.88
2.79-2.960.27291620.23561535X-RAY DIFFRACTION99.88
2.96-3.190.28261660.22521551X-RAY DIFFRACTION100
3.19-3.510.30071630.21351546X-RAY DIFFRACTION99.48
3.51-4.020.23731640.17971550X-RAY DIFFRACTION99.25
4.02-5.070.18541690.14711590X-RAY DIFFRACTION99.55
5.07-46.570.20211750.17181660X-RAY DIFFRACTION99.19
Refinement TLS params.Method: refined / Origin x: 8.33750124067 Å / Origin y: -24.2706634528 Å / Origin z: -13.621065723 Å
111213212223313233
T0.18755566333 Å2-0.00208543409533 Å2-0.047955546963 Å2-0.224489103534 Å2-0.0396907256858 Å2--0.178762022573 Å2
L1.83373247125 °20.0489701158439 °2-0.269018838709 °2-1.88242381228 °20.480927967745 °2--1.40904601165 °2
S0.185618790559 Å °-0.0696603684286 Å °0.0258543570939 Å °-0.0788958638963 Å °0.0952980397039 Å °-0.0447127239824 Å °0.0865321086507 Å °0.0873536925921 Å °-0.24690418446 Å °
Refinement TLS groupSelection details: all

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