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- PDB-8z6e: Structure of transcriptional regulator TetR -

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Basic information

Entry
Database: PDB / ID: 8z6e
TitleStructure of transcriptional regulator TetR
ComponentsTetR 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 / regulation of DNA-templated transcription / DNA binding / TetR family transcriptional regulator
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsHe, W. / Wen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No.82072237 China
CitationJournal: To Be Published
Title: Structure of transcriptional regulator TetR
Authors: He, W. / Wen, Y.
History
DepositionApr 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 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


Theoretical massNumber of molelcules
Total (without water)46,2212
Polymers46,2212
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-32 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.999, 47.760, 80.451
Angle α, β, γ (deg.)90.000, 98.570, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein TetR family transcriptional regulator / TetR/AcrR family transcriptional regulator / transcriptional regulator TetR2


Mass: 23110.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: AUO97_08420, F4T85_12235, FJU42_13590, HBK86_20440 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E3M4M0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.01 Å3/Da / Density % sol: 38.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Potassium citrate tribasic monohydrate, 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: Mar 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.97→34.01 Å / Num. obs: 25972 / % possible obs: 98.24 % / Redundancy: 5.4 % / Biso Wilson estimate: 32.17 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.087 / Net I/σ(I): 13.36
Reflection shellResolution: 1.97→2.04 Å / Num. unique obs: 2597 / CC1/2: 0.792

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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: 1.97→34.01 Å / SU ML: 0.2231 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8536
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2518 2019 7.85 %
Rwork0.2003 23712 -
obs0.2043 25731 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.46 Å2
Refinement stepCycle: LAST / Resolution: 1.97→34.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 0 161 3015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822921
X-RAY DIFFRACTIONf_angle_d0.9763957
X-RAY DIFFRACTIONf_chiral_restr0.0549443
X-RAY DIFFRACTIONf_plane_restr0.0068494
X-RAY DIFFRACTIONf_dihedral_angle_d5.4166379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.33811010.28451755X-RAY DIFFRACTION99.84
2.02-2.080.28942020.25081658X-RAY DIFFRACTION99.89
2.08-2.140.27951010.24061761X-RAY DIFFRACTION99.84
2.14-2.210.29552020.22381614X-RAY DIFFRACTION99.89
2.21-2.290.52441010.37281508X-RAY DIFFRACTION86.23
2.29-2.380.29791340.23861725X-RAY DIFFRACTION99.84
2.38-2.490.27821690.22531679X-RAY DIFFRACTION99.95
2.49-2.620.29561010.22221765X-RAY DIFFRACTION99.95
2.62-2.780.26062010.21691663X-RAY DIFFRACTION99.73
2.78-2.990.24231010.21121772X-RAY DIFFRACTION99.84
2.99-3.30.25812020.2041665X-RAY DIFFRACTION99.57
3.3-3.770.23151010.17471639X-RAY DIFFRACTION92.65
3.77-4.750.20751500.15861734X-RAY DIFFRACTION99.58
4.75-34.010.19081530.16961774X-RAY DIFFRACTION98.87
Refinement TLS params.Method: refined / Origin x: -2.73941012783 Å / Origin y: -1.21126550777 Å / Origin z: 22.1324814637 Å
111213212223313233
T0.158719946418 Å20.0200374425934 Å20.011480052925 Å2-0.152528195716 Å2-0.00606670674972 Å2--0.189913789628 Å2
L1.87017369207 °20.0790074150847 °20.126874448325 °2-0.729560803301 °2-0.262558130524 °2--1.28934811335 °2
S-0.00335762036708 Å °-0.110497306453 Å °0.0552873721139 Å °-0.00934866695086 Å °0.0280753402859 Å °-0.0130701012423 Å °-0.037864320005 Å °-0.02494641641 Å °-0.0179275829211 Å °
Refinement TLS groupSelection details: all

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