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- PDB-4b5p: Crystal structure of human alpha tubulin acetyltransferase cataly... -

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Basic information

Entry
Database: PDB / ID: 4b5p
TitleCrystal structure of human alpha tubulin acetyltransferase catalytic domain Q58A variant
Components(ALPHA-TUBULIN N-ACETYLTRANSFERASE) x 2
KeywordsTRANSFERASE / LYSINE ACETYLTRANSFERASE / ACETYL COA / TUBULIN / MICROTUBULES / CILIUM / INTRAFLAGELLAR TRANSPORT
Function / homology
Function and homology information


alpha-tubulin acetylation / alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / microtubule bundle / Cilium Assembly / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / NLRP3 inflammasome complex assembly / dentate gyrus development / regulation of fat cell differentiation / response to pain ...alpha-tubulin acetylation / alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / microtubule bundle / Cilium Assembly / L-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / NLRP3 inflammasome complex assembly / dentate gyrus development / regulation of fat cell differentiation / response to pain / positive regulation of NLRP3 inflammasome complex assembly / cilium assembly / neuron development / response to mechanical stimulus / clathrin-coated pit / regulation of microtubule cytoskeleton organization / microtubule cytoskeleton organization / mitotic spindle / 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
ACETYL COENZYME *A / Alpha-tubulin N-acetyltransferase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTaschner, M. / Vetter, M. / Lorentzen, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Atomic Resolution Structure of Human Alpha-Tubulin Acetyltransferase Bound to Acetyl-Coa.
Authors: Taschner, M. / Vetter, M. / Lorentzen, E.
History
DepositionAug 7, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Sep 11, 2013Group: Atomic model / Database references ...Atomic model / Database references / Other / Source and taxonomy / Structure summary
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)47,2496
Polymers45,5842
Non-polymers1,6654
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-35.6 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.760, 110.870, 113.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALPHA-TUBULIN N-ACETYLTRANSFERASE / ALPHA-TUBULIN ACETYLTRANSFERASE / ALPHA-TAT / TAT / ACETYLTRANSFERASE MEC-17 HOMOLOG


Mass: 22785.117 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-196 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5SQI0, alpha-tubulin N-acetyltransferase
#2: Protein ALPHA-TUBULIN N-ACETYLTRANSFERASE / ALPHA-TUBULIN ACETYLTRANSFERASE / ALPHA-TAT / TAT / ACETYLTRANSFERASE MEC-17 HOMOLOG


Mass: 22799.143 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1-196 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5SQI0, alpha-tubulin N-acetyltransferase
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.54 Å3/Da / Density % sol: 51.57 % / Description: NONE
Crystal growpH: 7 / Details: 2.8 M NA ACETATE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 60072 / % possible obs: 1 % / Observed criterion σ(I): -2 / Redundancy: 6.6 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.7
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.7 / % possible all: 0.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B5O

4b5o


Resolution: 1.6→39.669 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 22.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 1932 3.2 %
Rwork0.1849 --
obs0.1861 60020 96.37 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.684 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.2358 Å20 Å20 Å2
2--10.7152 Å20 Å2
3----6.4794 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 104 350 3404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013255
X-RAY DIFFRACTIONf_angle_d1.5874438
X-RAY DIFFRACTIONf_dihedral_angle_d18.3761233
X-RAY DIFFRACTIONf_chiral_restr0.39489
X-RAY DIFFRACTIONf_plane_restr0.006568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.29481110.33063305X-RAY DIFFRACTION79
1.64-1.68440.30621420.28354011X-RAY DIFFRACTION94
1.6844-1.7340.26181310.24644106X-RAY DIFFRACTION97
1.734-1.78990.3111340.23934107X-RAY DIFFRACTION97
1.7899-1.85390.251380.23464163X-RAY DIFFRACTION97
1.8539-1.92810.23961400.20154150X-RAY DIFFRACTION97
1.9281-2.01590.21781350.18234171X-RAY DIFFRACTION98
2.0159-2.12210.19281420.1674162X-RAY DIFFRACTION98
2.1221-2.25510.23291430.16834214X-RAY DIFFRACTION98
2.2551-2.42920.19931350.17094248X-RAY DIFFRACTION98
2.4292-2.67360.20361440.16984221X-RAY DIFFRACTION98
2.6736-3.06030.23161380.1894329X-RAY DIFFRACTION99
3.0603-3.85520.19181470.16944331X-RAY DIFFRACTION99
3.8552-39.6810.23231520.18294570X-RAY DIFFRACTION99
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)
12.3835-0.57720.42683.26941.2272.87250.05110.1990.1754-0.10950.06380.4724-0.3921-0.2489-0.18260.30740.05220.00690.23610.06510.2919-22.92083.032511.7626
22.5927-1.35471.294.905-3.38364.4217-0.0034-0.02660.532-0.25140.062-0.0213-0.4496-0.01190.00120.388-0.020.00360.1730.00470.3247-17.40336.39717.5465
32.6161-0.0715-0.18391.73960.33023.27530.07440.18780.1185-0.09-0.05650.0469-0.09190.0196-0.02250.14270.0056-0.01510.14150.01780.147-14.0186-8.869114.2302
45.679-1.548-1.5065.51682.46828.80630.65550.9915-0.4844-0.4849-0.56010.0774-0.0818-0.2873-0.2390.31060.0489-0.10090.4863-0.06480.251-14.3504-13.36721.1506
53.3665-0.6384-0.7731.62710.04862.0434-0.04660.3513-0.5730.00840.039-0.07790.22130.2703-0.00920.23730.0375-0.02540.2535-0.07340.2677-8.245-21.004814.6455
61.98740.2835-0.7921.7451-1.11392.8147-0.1899-0.0483-0.4333-0.14120.03980.11590.7278-0.18750.04250.3575-0.00780.01810.15290.0070.2806-21.9439-24.984642.2558
73.4843.621-0.5213.8359-0.23721.3541-0.2603-0.833-0.48830.01810.2506-0.3490.20240.3617-0.0640.21510.0843-0.00760.40450.04010.2856-3.0699-14.271452.6436
82.95830.00080.38511.09920.18032.5189-0.0494-0.17630.2266-0.0178-0.0436-0.12270.07960.26850.12310.15190.02620.0060.16620.00740.1809-12.396-10.144443.6283
94.92471.1667-0.60051.35810.07213.170.1157-0.49110.32030.0863-0.06860.1101-0.089-0.01020.010.1690.03870.00840.181-0.03040.187-18.2609-9.397850.2853
101.40330.80941.54861.07350.21612.5238-0.2396-0.13410.294-0.02680.1286-0.0701-0.39590.38160.0960.2278-0.0006-0.03740.2511-0.04710.2298-9.3754-1.505245.8769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID -1:26)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 34:56)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 57:145)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 146:150)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 151:190)
6X-RAY DIFFRACTION6(CHAIN B AND RESID -1:100)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 101:106)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 107:136)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 137:158)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 159:196)

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