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- PDB-4pk2: tubulin acetyltransferase complex with bisubstrate analog -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4pk2
Titletubulin acetyltransferase complex with bisubstrate analog
Components
  • ACETYL-SER-(N-PROPANOYL-LYS)-ASP--THR-NH2 PEPTIDE
  • Alpha-tubulin N-acetyltransferase 1
KeywordsTransferase/Peptide / tubulin / acetyltransferase / bisubstrate / coA / Transferase-Peptide complex
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.35 Å
AuthorsSzyk, A. / Roll-Mecak, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1ZIANS003122-04 United States
CitationJournal: Cell / Year: 2014
Title: Molecular basis for age-dependent microtubule acetylation by tubulin acetyltransferase.
Authors: Szyk, A. / Deaconescu, A.M. / Spector, J. / Goodman, B. / Valenstein, M.L. / Ziolkowska, N.E. / Kormendi, V. / Grigorieff, N. / Roll-Mecak, A.
History
DepositionMay 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Other
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
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: Alpha-tubulin N-acetyltransferase 1
B: ACETYL-SER-(N-PROPANOYL-LYS)-ASP--THR-NH2 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0413
Polymers23,2742
Non-polymers7681
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-3 kcal/mol
Surface area9890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.124, 52.483, 50.285
Angle α, β, γ (deg.)90.00, 106.83, 90.00
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: 22744.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATAT1, C6orf134, MEC17, Nbla00487 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SQI0, alpha-tubulin N-acetyltransferase
#2: Protein/peptide ACETYL-SER-(N-PROPANOYL-LYS)-ASP--THR-NH2 PEPTIDE


Mass: 529.566 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: With covalently linked COA, making bisubstrate analog
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-COA / COENZYME A


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


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris 8.5, 0.2M Ammonium Acetate, 25% Peg3350

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.347→35.535 Å / Num. obs: 40567 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Redundancy: 5.1 % / Rsym value: 0.07 / Net I/σ(I): 21.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementResolution: 1.35→35.535 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 16.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1682 2000 4.96 %
Rwork0.131 --
obs0.1329 40344 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati coordinate error free: 0.1 Å
Refinement stepCycle: LAST / Resolution: 1.35→35.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 48 253 1854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091773
X-RAY DIFFRACTIONf_angle_d1.6642444
X-RAY DIFFRACTIONf_dihedral_angle_d12.505717
X-RAY DIFFRACTIONf_chiral_restr0.078264
X-RAY DIFFRACTIONf_plane_restr0.007314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3501-1.38380.17141400.122533X-RAY DIFFRACTION92
1.3838-1.42120.16121350.12832746X-RAY DIFFRACTION100
1.4212-1.46310.21541440.12892731X-RAY DIFFRACTION100
1.4631-1.51030.19491470.11832728X-RAY DIFFRACTION100
1.5103-1.56430.18821410.11642768X-RAY DIFFRACTION100
1.5643-1.62690.13661390.10912763X-RAY DIFFRACTION100
1.6269-1.70090.15281460.10522733X-RAY DIFFRACTION100
1.7009-1.79060.16481420.10782755X-RAY DIFFRACTION100
1.7906-1.90280.14891470.1152756X-RAY DIFFRACTION100
1.9028-2.04970.17821370.11842763X-RAY DIFFRACTION100
2.0497-2.25590.15621440.12392764X-RAY DIFFRACTION100
2.2559-2.58230.15111460.13592780X-RAY DIFFRACTION100
2.5823-3.2530.18241520.14952768X-RAY DIFFRACTION100
3.253-35.54710.17291400.1482756X-RAY DIFFRACTION97

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