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- PDB-7f37: Crystal structure of AtaT2-AtaR2 complex -

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Basic information

Entry
Database: PDB / ID: 7f37
TitleCrystal structure of AtaT2-AtaR2 complex
Components
  • DUF1778 domain-containing protein
  • GNAT family N-acetyltransferase
KeywordsTRANSFERASE / Acetyltransferase / TOXIN
Function / homology: / :
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.896 Å
AuthorsYashiro, Y. / Tomita, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)LS136 Japan
Japan Society for the Promotion of Science (JSPS)18H03980 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)26113002 Japan
Japan Society for the Promotion of Science (JSPS)19K16069 Japan
CitationJournal: Cell Rep / Year: 2021
Title: Molecular basis of glycyl-tRNAGly acetylation by TacT from Salmonella Typhimurium
Authors: Yashiro, Y. / Zhang, C. / Sakaguchi, Y. / Suzuki, T. / Tomita, K.
History
DepositionJun 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 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.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: 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
B: GNAT family N-acetyltransferase
A: GNAT family N-acetyltransferase
C: DUF1778 domain-containing protein
D: DUF1778 domain-containing protein
F: DUF1778 domain-containing protein
E: DUF1778 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)79,2196
Polymers79,2196
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23380 Å2
ΔGint-155 kcal/mol
Surface area29440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.380, 62.210, 125.050
Angle α, β, γ (deg.)90.000, 105.980, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GNAT family N-acetyltransferase


Mass: 18741.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria)
Gene: Z4777, CQJ22_000873, E3157_02175, E3158_02185, E5F07_24590, FDZ86_02175
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U8MJD7
#2: Protein
DUF1778 domain-containing protein


Mass: 10433.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria)
Gene: CQJ22_000874, E3157_02180, E3158_02190, E3175_02180, E5F07_24585, FDZ86_02180
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7U8MLT5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Potassium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.896→46.12 Å / Num. obs: 17558 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.28 / Net I/σ(I): 7.5
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 1.92 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1708 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fvj

5fvj


Resolution: 2.896→45.375 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.3 / Stereochemistry target values: ML
Details: The reflection data set was anisotropically truncated and corrected using UCLA-DOE LAB Diffraction Anisotropy Server, and used for the refinement. Also, PDB extract was run using the ...Details: The reflection data set was anisotropically truncated and corrected using UCLA-DOE LAB Diffraction Anisotropy Server, and used for the refinement. Also, PDB extract was run using the anisotropically processed structure factor (.mtz) file.
RfactorNum. reflection% reflection
Rfree0.2832 739 5.03 %
Rwork0.2023 13955 -
obs0.2064 14694 83.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.73 Å2 / Biso mean: 37.6895 Å2 / Biso min: 3.85 Å2
Refinement stepCycle: final / Resolution: 2.896→45.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5141 0 0 6 5147
Biso mean---26.75 -
Num. residues----660
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8963-3.11990.3375770.2606129940
3.1199-3.43370.34941440.2422257978
3.4337-3.93030.30651710.19953324100
3.9303-4.95080.22881670.17483345100
4.9508-45.3750.27731800.20443408100

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