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- PDB-6rx9: Crystal structure of TetR from Acinetobacter baumannii AYE -

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Basic information

Entry
Database: PDB / ID: 6rx9
TitleCrystal structure of TetR from Acinetobacter baumannii AYE
ComponentsTetracycline repressor protein class G
KeywordsTRANSCRIPTION / Transcription regulation
Function / homology
Function and homology information


response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / 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
Similarity search - Domain/homology
Tetracycline repressor protein class G
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTam, H.K. / Sumyk, M. / Pos, K.M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Front Microbiol / Year: 2021
Title: Binding of Tetracyclines to Acinetobacter baumannii TetR Involves Two Arginines as Specificity Determinants
Authors: Sumyk, M. / Himpich, S. / Foong, W.E. / Herrmann, A. / Pos, K.M. / Tam, H.K.
History
DepositionJun 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 11, 2021Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetracycline repressor protein class G
B: Tetracycline repressor protein class G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5423
Polymers48,4462
Non-polymers961
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-53 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.330, 85.110, 62.350
Angle α, β, γ (deg.)90.000, 109.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tetracycline repressor protein class G


Mass: 24223.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain AYE) (bacteria)
Strain: AYE / Gene: tetR, ABAYE3639 / Variant: AYE / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Variant (production host): CE43(DE3) / References: UniProt: B0VCI2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 8.5
Details: 0.1 M Tris, pH8.5, 0.2 M Magnesium chloride hexahydrate, 0.2 M Sodium sulfate, and 25% PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→48.37 Å / Num. obs: 39419 / % possible obs: 99.7 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.017 / Rrim(I) all: 0.063 / Net I/σ(I): 20.3 / Num. measured all: 538887 / Scaling rejects: 3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 13.9 % / Num. unique obs: 2305 / CC1/2: 0.732 / Rpim(I) all: 0.518 / % possible all: 99.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A6I

1a6i


Resolution: 1.8→48.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.763 / SU ML: 0.115 / SU R Cruickshank DPI: 0.1377 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.127
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1939 4.9 %RANDOM
Rwork0.2079 ---
obs0.2093 37479 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 94.45 Å2 / Biso mean: 42.823 Å2 / Biso min: 25.47 Å2
Baniso -1Baniso -2Baniso -3
1-2.1 Å2-0 Å20.3 Å2
2---1.36 Å20 Å2
3----0.76 Å2
Refinement stepCycle: final / Resolution: 1.8→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3003 0 5 188 3196
Biso mean--86.33 48.05 -
Num. residues----379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133089
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172864
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.6364175
X-RAY DIFFRACTIONr_angle_other_deg1.1441.5766601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5375382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91620.86186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21115524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9441531
X-RAY DIFFRACTIONr_chiral_restr0.0420.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02721
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 134 -
Rwork0.379 2742 -
all-2876 -
obs--99.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3448-0.153-0.25981.18650.49233.6159-0.04780.04680.0614-0.08730.053-0.0455-0.0442-0.1905-0.00520.12050.01080.01480.02580.00930.0167-2.66095.07297.263
21.1563-0.4839-0.08043.11130.87681.3898-0.0091-0.0141-0.07940.06010.058-0.32070.10250.1522-0.04890.11010.0005-0.00570.01850.00070.05075.2282-8.243220.0215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 205
2X-RAY DIFFRACTION2B3 - 205

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