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- PDB-4u9z: Structure of the alpha-tubulin acetyltransferase alpha-TAT1/Mec-1... -

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Basic information

Entry
Database: PDB / ID: 4u9z
TitleStructure of the alpha-tubulin acetyltransferase alpha-TAT1/Mec-17 in complex with CoA
ComponentsAlpha-tubulin N-acetyltransferase 1
KeywordsTRANSFERASE / GNAT superfamily fold
Function / homology
Function and homology information


alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / alpha-tubulin acetylation / microtubule bundle / Cilium Assembly / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / NLRP3 inflammasome complex assembly / dentate gyrus development / regulation of fat cell differentiation / positive regulation of NLRP3 inflammasome complex assembly ...alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / alpha-tubulin acetylation / microtubule bundle / Cilium Assembly / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / NLRP3 inflammasome complex assembly / dentate gyrus development / regulation of fat cell differentiation / positive regulation of NLRP3 inflammasome complex assembly / response to pain / cilium assembly / neuron development / regulation of microtubule cytoskeleton organization / response to mechanical stimulus / clathrin-coated pit / mitotic spindle / microtubule cytoskeleton organization / spermatogenesis / microtubule / axon / focal adhesion / Golgi apparatus / cytosol
Similarity search - Function
Gcn5-related N-acetyltransferase (GNAT) domain, ATAT-type / Alpha-tubulin N-acetyltransferase / GNAT acetyltransferase, Mec-17 / Alpha-tubulin Gcn5-related N-acetyltransferase (GNAT) domain profile. / Gcn5-related N-acetyltransferase (GNAT) / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Alpha-tubulin N-acetyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsYuzawa, S. / Sumimoto, H.
CitationJournal: To Be Published
Title: Structure of alpha-TAT1/Mec-17 in complex with CoA
Authors: Yuzawa, S. / Kamakura, S. / Sumimoto, H.
History
DepositionAug 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

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Assembly

Deposited unit
A: Alpha-tubulin N-acetyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7012
Polymers22,9331
Non-polymers7681
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-1 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.645, 34.329, 64.226
Angle α, β, γ (deg.)90.000, 103.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-tubulin N-acetyltransferase 1 / TAT / Acetyltransferase mec-17 homolog


Mass: 22933.211 Da / Num. of mol.: 1 / Fragment: UNP residues 1-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAT1, C6orf134, MEC17, Nbla00487 / Plasmid: pRSFDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5SQI0, alpha-tubulin N-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1M Tris, 25% PEG 3350

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17372 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.39 Å2 / Rmerge(I) obs: 0.084 / Χ2: 1.042 / Net I/av σ(I): 12.121 / Net I/σ(I): 11.2 / Num. measured all: 63548
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.833.60.3678501.083100
1.83-1.863.70.3138511.076100
1.86-1.93.60.2868721.085100
1.9-1.943.70.2798401.056100
1.94-1.983.70.2078911.075100
1.98-2.033.60.1888661.034100
2.03-2.083.70.1948631.086100
2.08-2.133.70.1488820.996100
2.13-2.23.70.1348291.022100
2.2-2.273.70.1598621.058100
2.27-2.353.70.1218540.963100
2.35-2.443.70.1128760.999100
2.44-2.553.70.1058751.018100
2.55-2.693.70.18711.043100
2.69-2.863.70.0898701.068100
2.86-3.083.70.0788771.083100
3.08-3.393.70.0718760.978100
3.39-3.883.70.0648761.08199.9
3.88-4.883.60.0558900.99199.2
4.88-503.40.0579011.03897.2

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Processing

Software
NameVersionClassification
HKL-2000data processing
HKL-2000data scaling
PHASER2.4.0phasing
Coot0.7-predata extraction
PHENIXphenix.refine: 1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VWD

3vwd


Resolution: 1.802→31.976 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 878 5.06 %
Rwork0.2159 16482 -
obs0.2181 17360 99.57 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.01 Å2 / Biso mean: 25.1548 Å2 / Biso min: 8.62 Å2
Refinement stepCycle: final / Resolution: 1.802→31.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1461 0 48 102 1611
Biso mean--26.41 31.76 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011605
X-RAY DIFFRACTIONf_angle_d1.3312185
X-RAY DIFFRACTIONf_chiral_restr0.059237
X-RAY DIFFRACTIONf_plane_restr0.006283
X-RAY DIFFRACTIONf_dihedral_angle_d18.998616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8015-1.91440.31041530.23812684283799
1.9144-2.06210.2651320.233127232855100
2.0621-2.26960.31171540.2227302884100
2.2696-2.59790.2921340.223527672901100
2.5979-3.27260.2931470.22627682915100
3.2726-31.98070.20181580.19842810296899

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