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- PDB-4h6z: Tubulin acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 4h6z
TitleTubulin acetyltransferase
ComponentsAlpha-tubulin N-acetyltransferase
KeywordsTRANSFERASE / tubulin acetyltransferase
Function / homology
Function and homology information


alpha-tubulin acetylation / alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / neuron development / clathrin-coated pit / regulation of microtubule cytoskeleton organization / microtubule cytoskeleton organization / spindle / microtubule ...alpha-tubulin acetylation / alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / neuron development / clathrin-coated pit / regulation of microtubule cytoskeleton organization / microtubule cytoskeleton organization / spindle / microtubule / axon / focal adhesion / cytoplasm
Similarity search - Function
Rhinovirus 14, subunit 4 - #120 / Rhinovirus 14, subunit 4 / 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. / Other non-globular / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase ...Rhinovirus 14, subunit 4 - #120 / Rhinovirus 14, subunit 4 / 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. / Other non-globular / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / PHOSPHATE ION / Alpha-tubulin N-acetyltransferase 1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.701 Å
AuthorsKizub, L. / Szyk, A. / Piszczek, G. / Roll-Mecak, A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structures of tubulin acetyltransferase reveal a conserved catalytic core and the plasticity of the essential N terminus.
Authors: Kormendi, V. / Szyk, A. / Piszczek, G. / Roll-Mecak, A.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,8956
Polymers43,0862
Non-polymers1,8094
Water23413
1
A: Alpha-tubulin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5434
Polymers21,5431
Non-polymers1,0003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-tubulin N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3532
Polymers21,5431
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-20 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.488, 81.488, 117.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 21543.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: atat1, mec17, si:ch211-152p11.5, zgc:65893 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6PH17, alpha-tubulin N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES pH 6.0, 0.6 M NaH2PO4 and KH2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9806, 0.9637
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98061
20.96371
ReflectionResolution: 2.7→50 Å / Num. all: 11419 / Num. obs: 11419 / % possible obs: 100 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6
Reflection shellResolution: 2.7→2.75 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.701→47.71 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 23.79 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2382 571 5 %
Rwork0.219 --
obs0.222 11419 99.97 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.701→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 112 13 2440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052487
X-RAY DIFFRACTIONf_angle_d0.8533382
X-RAY DIFFRACTIONf_dihedral_angle_d23.819888
X-RAY DIFFRACTIONf_chiral_restr0.047365
X-RAY DIFFRACTIONf_plane_restr0.003418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.701-2.97280.32531390.26642633X-RAY DIFFRACTION100
2.9728-3.40290.31291400.22512673X-RAY DIFFRACTION100
3.4029-4.28680.1881420.20742694X-RAY DIFFRACTION100
4.2868-47.71740.2271500.21862848X-RAY DIFFRACTION100

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