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- PDB-6ajn: Crystal structure of AtaTR bound with AcCoA -

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Basic information

Entry
Database: PDB / ID: 6ajn
TitleCrystal structure of AtaTR bound with AcCoA
Components
  • DUF1778 domain-containing protein
  • N-acetyltransferase
KeywordsTOXIN / Antitoxin / Acetyltransferas
Function / homology
Function and homology information


toxin sequestering activity / regulation of DNA-templated transcription
Similarity search - Function
Vibrio phage ICP1, Orf50 / Protein of unknown function (DUF1778) / Acetyltransferase (GNAT) domain / Ribbon-helix-helix / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / N-acetyltransferase / DUF1778 domain-containing protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.302 Å
AuthorsYashiro, Y. / Yamashita, S. / Tomita, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science18H03980 Japan
Japan Society for the Promotion of Science26113002 Japan
CitationJournal: Structure / Year: 2019
Title: Crystal Structure of the Enterohemorrhagic Escherichia coli AtaT-AtaR Toxin-Antitoxin Complex.
Authors: Yashiro, Y. / Yamashita, S. / Tomita, K.
History
DepositionAug 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyltransferase
B: N-acetyltransferase
C: DUF1778 domain-containing protein
D: DUF1778 domain-containing protein
E: DUF1778 domain-containing protein
F: DUF1778 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2398
Polymers75,6206
Non-polymers1,6192
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19080 Å2
ΔGint-133 kcal/mol
Surface area31490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.750, 117.080, 77.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein N-acetyltransferase


Mass: 19371.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: BWP17_00640, CVH05_12355 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V3CQ74
#2: Protein
DUF1778 domain-containing protein / Toxin-antitoxin system protein / Toxin-antitoxin system / antitoxin component / ribbon-helix-helix ...Toxin-antitoxin system protein / Toxin-antitoxin system / antitoxin component / ribbon-helix-helix fold protein / Ybl13


Mass: 9219.421 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ybl13, ybl13_1, A8G17_04185, AA102_09360, AC789_1c38270, ACN002_3543, ACN81_27750, ACU90_15595, AM270_07745, ARC77_13665, AU473_04475, B1K96_23180, B1K96_30445, BHS81_20640, BIZ41_06975, BK292_ ...Gene: ybl13, ybl13_1, A8G17_04185, AA102_09360, AC789_1c38270, ACN002_3543, ACN81_27750, ACU90_15595, AM270_07745, ARC77_13665, AU473_04475, B1K96_23180, B1K96_30445, BHS81_20640, BIZ41_06975, BK292_07330, BMT53_16880, BN17_33961, BTQ04_07040, BWP17_00645, C5P43_28430, C5Y95_12220, C6986_22200, C7B02_13210, COD46_18440, CR538_01655, CVH05_12360, CXB56_05005, ERS085366_00076, ERS085374_01548, ERS085383_01733, ERS085404_01502, RX35_03224, SAMEA3472031_01067, SAMEA3472035_01725, SAMEA3472046_03089, SAMEA3472089_01664, SAMEA3472114_02231, SAMEA3472140_01493, SAMEA3472152_01575, SAMEA3484446_02490, SAMEA3485110_02685, SAMEA3753064_01902, SAMEA3753068_03922, SAMEA3753290_02356
Production host: Escherichia coli (E. coli) / References: UniProt: J7QA90
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S

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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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 100 mM Tris-HCl pH 8.6, 16% PEG3350, 2% Tacsimate

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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: Nov 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.3→19.874 Å / Num. obs: 14321 / % possible obs: 99.8 % / Redundancy: 12.934 % / Biso Wilson estimate: 87.68 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.264 / Rrim(I) all: 0.275 / Χ2: 0.86 / Net I/σ(I): 8.68 / Num. measured all: 185225 / Scaling rejects: 5
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
3.3-3.3913.2081.751.6413565105210270.7271.8297.6
3.39-3.4813.6941.4582.1713817100910090.7191.515100
3.48-3.5813.4981.0872.85133909929920.8381.129100
3.58-3.6913.3640.8623.52127639559550.8580.896100
3.69-3.8112.9460.7034.15119239219210.9140.732100
3.81-3.9512.360.565.01111869059050.9460.584100
3.95-4.112.7080.4286.16112218838830.9850.446100
4.1-4.2613.5510.3398.23112888338330.9820.353100
4.26-4.4513.4480.25410.42108268058050.9880.264100
4.45-4.6713.2390.22511.39105387967960.9930.234100
4.67-4.9212.9450.20711.6193727247240.9930.215100
4.92-5.2212.2180.22210.8186877117110.9890.232100
5.22-5.5812.8490.2410.4185836686680.9880.25100
5.58-6.0313.4890.21710.9481346046030.9950.22599.8
6.03-6.613.0840.18912.1874715715710.9960.197100
6.6-7.3812.0470.14115.3764215335330.9950.148100
7.38-8.5311.660.119.4654804704700.9970.105100
8.53-10.4412.5330.07924.1150134004000.9980.083100
10.44-14.7711.0710.0725.7335873243240.9980.073100
14.77-19.87410.2620.07421.9219601991910.9980.07896

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Processing

Software
NameVersionClassification
PHENIX1.12-2829_1309refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AJM

6ajm


Resolution: 3.302→19.874 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 36.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3381 711 5 %
Rwork0.2782 13517 -
obs0.281 14228 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 242.57 Å2 / Biso mean: 104.616 Å2 / Biso min: 43.32 Å2
Refinement stepCycle: final / Resolution: 3.302→19.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4946 0 102 0 5048
Biso mean--114.04 --
Num. residues----623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045126
X-RAY DIFFRACTIONf_angle_d1.1026934
X-RAY DIFFRACTIONf_chiral_restr0.148785
X-RAY DIFFRACTIONf_plane_restr0.004890
X-RAY DIFFRACTIONf_dihedral_angle_d17.0283140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3023-3.55590.36271390.35832641278099
3.5559-3.91130.37541400.326626712811100
3.9113-4.47160.3211400.260926602800100
4.4716-5.61270.3431430.259127262869100
5.6127-19.87430.32371490.257928192968100
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)
13.04341.91072.02936.87620.7055.69460.6403-1.2581-0.37070.9134-0.2233-0.86080.6301-0.0965-0.19060.92560.0541-0.06410.9228-0.05260.5636.205862.082387.2458
21.4791-1.1342-0.60017.8471-2.34962.5635-1.43460.74650.8264-1.5463-0.19022.13950.0107-0.72980.96531.7230.3058-0.10871.22360.20531.118516.470248.92155.9263
34.67093.5571.59345.65093.84328.72660.4975-1.0565-0.32740.9633-0.96830.25040.7753-2.03140.52290.8983-0.13470.09931.0894-0.0680.631220.790160.838480.2732
44.3141-1.01611.28956.0272-6.63487.30960.75513.1961-2.0328-0.95360.45210.68183.6943.9435-1.59510.80790.3168-0.22581.3705-0.45570.975736.3897-2.468525.5664
59.52181.15572.65386.6444-3.18952.79310.48441.0285-0.6716-1.30650.3663-1.4378-0.62110.5995-0.96891.14360.21570.24881.0948-0.34240.915241.45869.567324.2321
68.21492.28970.73977.00184.59125.35260.04930.25560.6394-0.75840.3918-0.9017-0.34160.4352-0.39740.68880.1830.17790.60840.01070.779539.983312.994431.1336
74.3437.6597-2.37212.0083-3.52961.58790.37780.7964-1.2642-1.31860.2995-2.8164-0.28582.1556-0.92211.80380.0597-0.09611.4481-0.38390.756142.63011.446221.8746
82.8442-0.8229-0.61382.8255-0.73364.46180.5880.1916-0.0640.2520.56610.71390.95690.07370.71650.7763-0.27150.23170.5670.12570.152431.55712.210638.9747
94.7826-2.75-2.6034.42123.74955.5599-0.1162-0.7963-0.5177-0.21161.316-0.9577-0.92361.5466-0.2371-0.9549-0.8333-1.74821.39210.2884-0.237426.55816.621448.234
106.73354.34050.12386.20441.58797.85541.06720.19361.6751-2.4991-1.70031.4958-0.8497-1.1587-0.01781.17390.47660.0181.12670.0520.724328.68378.733222.4663
115.479-0.60391.88194.73533.49395.0090.25650.4912-0.576-0.31820.43910.65521.5263-0.272-0.44190.9433-0.0946-0.19260.5980.03540.447527.03856.233238.9219
127.1874-3.7905-5.60873.90852.93484.2370.1940.66470.4025-1.0759-0.1423-0.0655-0.3885-1.8235-0.29220.68890.0202-0.25830.986-0.05070.744718.140216.299433.9524
133.4138-2.86780.80853.51180.78252.0790.1346-0.2343-1.43350.34251.03952.883-0.22170.3325-1.48560.7221-0.18640.0730.7276-0.01340.961320.08473.848742.4821
147.97152.82680.20633.5642.37928.977-0.01270.2941-0.75890.50930.2776-1.8838-0.31271.1366-0.44940.6535-0.11780.08050.7804-0.0761.18953.956133.948268.597
156.0608-6.1509-2.80026.19823.46025.25880.77-0.1075-1.36440.3955-0.92830.6478-0.8709-0.21390.07351.0946-0.3492-0.11450.634-0.08491.164742.25542.394166.7731
166.6001-2.92040.16948.37723.74544.6786-0.0305-0.89640.19960.7842-0.73071.20380.6697-0.68770.74930.7246-0.2318-0.12941.7369-0.06950.794713.377254.285970.0801
172.053-0.633-0.96947.98173.91133.0244-0.9472-0.5559-0.66491.0208-2.0383.39020.664-1.4627-0.01011.03221.39690.21282.1423-0.24781.171816.337872.721485.7845
189.3108-2.6899-0.43373.27884.62788.62270.04730.60180.7163-1.6432-0.008-1.9296-1.390.3336-0.14921.1049-0.15830.12080.55010.14491.211152.031441.683543.8879
195.23287.17256.75849.35478.66079.71111.79130.0821-0.34441.1154-0.9645-0.01211.61390.0953-0.42540.52660.12970.06690.6154-0.04060.871443.198430.530947.3954
205.1331-2.0006-1.468.2825.94667.4702-0.16820.1807-0.3383-0.23390.40930.90270.7666-1.0268-0.22990.7837-0.2234-0.2110.96820.26730.730517.49379.086541.0194
215.28412.15872.7385.6645-0.59432.20650.0883-0.09510.7580.2439-0.3269-0.37450.13870.39910.07790.8508-0.1021-0.3550.70930.04370.993849.461245.370271.9413
222.67595.12055.45728.13549.04459.0842-0.4193-0.29840.45771.696-1.15221.65831.4968-0.79711.3411.2972-0.0186-0.25980.672-0.09880.990741.544721.983760.0897
238.2561-3.95912.7577.1814-2.10985.86040.27131.2767-2.6778-0.2083-0.63150.14071.4350.41230.02430.72790.02720.18620.6487-0.2031.205949.507229.461639.774
246.4337-7.8117-7.67767.90348.15687.1355-0.07120.1591-0.1499-0.1096-0.2702-0.1359-0.3943-0.33710.07780.6851-0.19540.05190.6431-0.04690.738939.106850.434655.4854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 69 )A1 - 69
2X-RAY DIFFRACTION2chain 'A' and (resid 70 through 87 )A70 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 172 )A88 - 172
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 8 )B1 - 8
5X-RAY DIFFRACTION5chain 'B' and (resid 9 through 24 )B9 - 24
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 51 )B25 - 51
7X-RAY DIFFRACTION7chain 'B' and (resid 52 through 59 )B52 - 59
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 69 )B60 - 69
9X-RAY DIFFRACTION9chain 'B' and (resid 70 through 93 )B70 - 93
10X-RAY DIFFRACTION10chain 'B' and (resid 94 through 106 )B94 - 106
11X-RAY DIFFRACTION11chain 'B' and (resid 107 through 137 )B107 - 137
12X-RAY DIFFRACTION12chain 'B' and (resid 138 through 158 )B138 - 158
13X-RAY DIFFRACTION13chain 'B' and (resid 159 through 172 )B159 - 172
14X-RAY DIFFRACTION14chain 'C' and (resid 6 through 31 )C6 - 31
15X-RAY DIFFRACTION15chain 'C' and (resid 32 through 52 )C32 - 52
16X-RAY DIFFRACTION16chain 'C' and (resid 53 through 75 )C53 - 75
17X-RAY DIFFRACTION17chain 'C' and (resid 76 through 86 )C76 - 86
18X-RAY DIFFRACTION18chain 'D' and (resid 6 through 31 )D6 - 31
19X-RAY DIFFRACTION19chain 'D' and (resid 32 through 52 )D32 - 52
20X-RAY DIFFRACTION20chain 'D' and (resid 53 through 86 )D53 - 86
21X-RAY DIFFRACTION21chain 'E' and (resid 6 through 31 )E6 - 31
22X-RAY DIFFRACTION22chain 'E' and (resid 32 through 71 )E32 - 71
23X-RAY DIFFRACTION23chain 'F' and (resid 6 through 31 )F6 - 31
24X-RAY DIFFRACTION24chain 'F' and (resid 32 through 71 )F32 - 71

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