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- PDB-7chd: AtaT complexed with acetyl-methionyl-tRNAfMet -

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Basic information

Entry
Database: PDB / ID: 7chd
TitleAtaT complexed with acetyl-methionyl-tRNAfMet
Components
  • N-acetyltransferase domain-containing protein
  • RNA (77-MER)
KeywordsTRANSFERASE / Acetyltranferase / TOXIN
Function / homologyAcetyltransferase (GNAT) domain / N-acetyltransferase activity / GNAT domain / Acyl-CoA N-acyltransferase / RNA / RNA (> 10) / N-acetyltransferase domain-containing protein
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.804 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: Nat Commun / Year: 2020
Title: Mechanism of aminoacyl-tRNA acetylation by an aminoacyl-tRNA acetyltransferase AtaT from enterohemorrhagic E. coli.
Authors: Yashiro, Y. / Sakaguchi, Y. / Suzuki, T. / Tomita, K.
History
DepositionJul 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 18, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetyltransferase domain-containing protein
B: N-acetyltransferase domain-containing protein
C: N-acetyltransferase domain-containing protein
D: N-acetyltransferase domain-containing protein
E: N-acetyltransferase domain-containing protein
F: N-acetyltransferase domain-containing protein
G: N-acetyltransferase domain-containing protein
H: N-acetyltransferase domain-containing protein
I: RNA (77-MER)
J: RNA (77-MER)


Theoretical massNumber of molelcules
Total (without water)216,31210
Polymers216,31210
Non-polymers00
Water00
1
G: N-acetyltransferase domain-containing protein
I: RNA (77-MER)

G: N-acetyltransferase domain-containing protein
I: RNA (77-MER)


  • defined by author&software
  • Evidence: gel filtration, We confirmed the protein dimer formation by gel-filtration., native gel electrophoresis, The RNA molecule is a known substrate for the protein enzyme. Also, we observed ...Evidence: gel filtration, We confirmed the protein dimer formation by gel-filtration., native gel electrophoresis, The RNA molecule is a known substrate for the protein enzyme. Also, we observed binding of the protein to the RNA by electrophoretic mobility shift assay.
  • 91.3 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)91,3274
Polymers91,3274
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9890 Å2
ΔGint-52 kcal/mol
Surface area39730 Å2
MethodPISA
2
H: N-acetyltransferase domain-containing protein
J: RNA (77-MER)

H: N-acetyltransferase domain-containing protein
J: RNA (77-MER)


Theoretical massNumber of molelcules
Total (without water)91,3274
Polymers91,3274
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area9730 Å2
ΔGint-52 kcal/mol
Surface area38770 Å2
MethodPISA
3
A: N-acetyltransferase domain-containing protein
B: N-acetyltransferase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)41,6622
Polymers41,6622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-11 kcal/mol
Surface area18640 Å2
MethodPISA
4
C: N-acetyltransferase domain-containing protein
D: N-acetyltransferase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)41,6622
Polymers41,6622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-13 kcal/mol
Surface area18520 Å2
MethodPISA
5
E: N-acetyltransferase domain-containing protein
F: N-acetyltransferase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)41,6622
Polymers41,6622
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-9 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)269.830, 68.280, 136.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 64 or resid 66 through 172))
21(chain B and (resid 5 through 64 or resid 66 through 172))
31(chain C and (resid 5 through 64 or resid 66 through 172))
41(chain D and (resid 5 through 64 or resid 66 through 172))
51(chain E and (resid 5 through 64 or resid 66 through 172))
61(chain F and (resid 5 through 64 or resid 66 through 172))
71(chain G and (resid 5 through 64 or resid 66 through 172))
81(chain H and (resid 5 through 64 or resid 66 through 172))
12chain I
22chain J

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRLEULEU(chain A and (resid 5 through 64 or resid 66 through 172))AA5 - 645 - 64
121GLYGLYTHRTHR(chain A and (resid 5 through 64 or resid 66 through 172))AA66 - 17266 - 172
211THRTHRLEULEU(chain B and (resid 5 through 64 or resid 66 through 172))BB5 - 645 - 64
221GLYGLYTHRTHR(chain B and (resid 5 through 64 or resid 66 through 172))BB66 - 17266 - 172
311THRTHRLEULEU(chain C and (resid 5 through 64 or resid 66 through 172))CC5 - 645 - 64
321GLYGLYTHRTHR(chain C and (resid 5 through 64 or resid 66 through 172))CC66 - 17266 - 172
411THRTHRLEULEU(chain D and (resid 5 through 64 or resid 66 through 172))DD5 - 645 - 64
421GLYGLYTHRTHR(chain D and (resid 5 through 64 or resid 66 through 172))DD66 - 17266 - 172
511THRTHRLEULEU(chain E and (resid 5 through 64 or resid 66 through 172))EE5 - 645 - 64
521GLYGLYTHRTHR(chain E and (resid 5 through 64 or resid 66 through 172))EE66 - 17266 - 172
611THRTHRLEULEU(chain F and (resid 5 through 64 or resid 66 through 172))FF5 - 645 - 64
621GLYGLYTHRTHR(chain F and (resid 5 through 64 or resid 66 through 172))FF66 - 17266 - 172
711THRTHRLEULEU(chain G and (resid 5 through 64 or resid 66 through 172))GG5 - 645 - 64
721GLYGLYTHRTHR(chain G and (resid 5 through 64 or resid 66 through 172))GG66 - 17266 - 172
811THRTHRLEULEU(chain H and (resid 5 through 64 or resid 66 through 172))HH5 - 645 - 64
821GLYGLYTHRTHR(chain H and (resid 5 through 64 or resid 66 through 172))HH66 - 17266 - 172
112CCCCchain III1 - 741 - 75
212CCCCchain JJJ1 - 741 - 75

NCS ensembles :
ID
1
2

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Components

#1: Protein
N-acetyltransferase domain-containing protein


Mass: 20830.770 Da / Num. of mol.: 8 / Mutation: G108D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: O157:H7 / Gene: Z4832 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8XED1
#2: RNA chain RNA (77-MER)


Mass: 24832.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
Has ligand of interestN

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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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Hepes 6.8, 0.2M Sodium formate, 10% PEG3350, 0.5% Jeffemine

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Mar 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.8→48.214 Å / Num. obs: 25540 / % possible obs: 99.8 % / Redundancy: 26.161 % / Biso Wilson estimate: 127.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.441 / Rrim(I) all: 0.449 / Χ2: 0.661 / Net I/σ(I): 8.36 / Num. measured all: 668160 / Scaling rejects: 76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.8-3.926.1853.4161.2547473183218130.4683.48399
3.9-4.0127.3972.9581.650384183918390.6323.013100
4.01-4.1327.7152.6191.7947891172817280.7312.667100
4.13-4.2527.141.9352.5147223174017400.8271.972100
4.25-4.3927.0721.2893.5544480164316430.9171.313100
4.39-4.5526.2171.064.2342471162016200.9351.081100
4.55-4.7225.1560.8924.7338488153015300.9410.911100
4.72-4.9126.6330.8015.5440909153715360.9560.81799.9
4.91-5.1325.5950.7415.7936064140914090.9580.756100
5.13-5.3827.6270.7226.2538512139413940.9710.735100
5.38-5.6727.2340.5997.536384133613360.9810.611100
5.67-6.0126.9840.5468.0333163123012290.9840.55699.9
6.01-6.4326.1190.5028.2831056118911890.9840.512100
6.43-6.9524.2130.35610.4427070111811180.9920.364100
6.95-7.6124.9850.25913.3325810103310330.9960.264100
7.61-8.5125.8380.15220.18242629399390.9990.155100
8.51-9.8225.630.09728.61211458258250.9990.099100
9.82-12.0324.030.07135.93170857117110.9990.072100
12.03-17.0121.1860.05837.691239458558510.06100
17.01-48.21418.2540.08331.78589634232310.08694.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GTP

6gtp


Resolution: 3.804→48.214 Å / SU ML: 0.67 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 41.35 / Stereochemistry target values: ML
Details: N-acetylmethionine was covalently attached to 3'O of A76 (aminoacylation), although the electron density for C75A76-acetylmethionine was not observed, thus not included in the model.
RfactorNum. reflection% reflection
Rfree0.3409 1273 4.99 %
Rwork0.2862 24215 -
obs0.2892 25488 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 259.16 Å2 / Biso mean: 139.9518 Å2 / Biso min: 45.15 Å2
Refinement stepCycle: final / Resolution: 3.804→48.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10966 3206 0 0 14172
Num. residues----1528
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6501X-RAY DIFFRACTION9.811TORSIONAL
12B6501X-RAY DIFFRACTION9.811TORSIONAL
13C6501X-RAY DIFFRACTION9.811TORSIONAL
14D6501X-RAY DIFFRACTION9.811TORSIONAL
15E6501X-RAY DIFFRACTION9.811TORSIONAL
16F6501X-RAY DIFFRACTION9.811TORSIONAL
17G6501X-RAY DIFFRACTION9.811TORSIONAL
18H6501X-RAY DIFFRACTION9.811TORSIONAL
21I1794X-RAY DIFFRACTION9.811TORSIONAL
22J1794X-RAY DIFFRACTION9.811TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.8041-3.95630.45671360.399260099
3.9563-4.13630.39361400.36432643100
4.1363-4.35420.38651400.3152656100
4.3542-4.62680.38061400.29562670100
4.6268-4.98370.35391400.28572653100
4.9837-5.48460.33811420.27962690100
5.4846-6.27680.35961420.2782714100
6.2768-7.90250.33121430.29272722100
7.9025-48.210.28711500.2422286799

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