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- PDB-4h6u: Tubulin acetyltransferase mutant -

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Basic information

Entry
Database: PDB / ID: 4h6u
TitleTubulin acetyltransferase mutant
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
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) / Acyl-CoA N-acyltransferase / Aminopeptidase / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4482 Å
AuthorsRoll-Mecak, A. / Kizub, V. / Szyk, 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 1.3Jul 22, 2015Group: Structure summary
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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)46,4606
Polymers44,7072
Non-polymers1,7534
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-45 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.128, 58.128, 225.070
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: 22353.520 Da / Num. of mol.: 2 / Mutation: D117A
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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE REFERENCE SEQUENCE IS BASED ON A VARIANT

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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: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.65M NaH2PO4 and KH2PO4, pH 6.5, 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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 15066 / Num. obs: 15066 / % possible obs: 99.9 % / Observed criterion σ(F): 3.6 / Observed criterion σ(I): 3.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H6Z

4h6z


Resolution: 2.4482→29.064 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 753 5 %
Rwork0.1964 --
obs0.199 15065 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4482→29.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 108 41 2692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152718
X-RAY DIFFRACTIONf_angle_d1.5243699
X-RAY DIFFRACTIONf_dihedral_angle_d22.294982
X-RAY DIFFRACTIONf_chiral_restr0.076398
X-RAY DIFFRACTIONf_plane_restr0.01466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4482-2.63710.30081450.20272764X-RAY DIFFRACTION100
2.6371-2.90220.25091480.20842801X-RAY DIFFRACTION100
2.9022-3.32170.28521470.20022808X-RAY DIFFRACTION100
3.3217-4.1830.22841530.18032882X-RAY DIFFRACTION100
4.183-29.0660.23861600.2023057X-RAY DIFFRACTION100
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)
16.97838.14-0.08852.2870.44633.53020.1210.405-0.04880.2698-0.0801-1.0130.31940.59720.08760.36380.075-0.08530.44620.08450.638167.861826.827699.6586
27.92665.0125-0.92552.155-5.44424.19340.29210.25130.82510.5894-0.54450.5333-0.70730.60170.36840.5223-0.1278-0.11040.46760.0210.544465.976644.1269106.7412
33.95240.62665.46284.04272.17739.72110.1560.11730.01870.1595-0.15540.37030.18150.15360.00830.2027-0.0296-0.03340.40390.1280.396464.347736.315990.912
41.70610.15261.32654.13890.49626.4653-0.19820.41620.3291-0.058-0.02280.3406-0.20970.26130.12010.2475-0.0067-0.07560.37980.15570.388662.109142.024384.9124
59.8562-2.92876.29525.9933-0.03938.18390.19880.4746-0.0157-0.2025-0.3674-0.13410.1130.42370.08270.2248-0.0006-0.00540.52520.07440.239461.809940.774378.1638
61.5938-1.0190.29443.5295-1.49052.01460.1017-0.2085-0.19010.4442-0.1486-0.3745-0.10690.28620.03460.3028-0.1176-0.16360.48450.06510.422364.002728.8765108.6752
77.06660.12191.18312.870.84542.9888-0.02640.18560.5519-0.0179-0.16240.0064-0.29740.09990.19470.2888-0.0712-0.02560.30830.0870.291449.383826.8324102.0363
87.7485-2.74363.04825.9625-1.86265.7937-0.1252-0.79640.29370.53670.0643-0.4288-0.4753-0.07830.04450.3352-0.0848-0.05350.31660.00880.263346.897725.5525110.8874
97.4641-5.48613.07332.1791-0.87517.5734-0.08-0.2268-0.16170.4719-0.0949-0.2009-0.1052-0.26430.04960.3637-0.1282-0.09430.35930.03110.29842.269217.5933104.0993
108.7492.2636.70737.32291.94168.01230.36120.281-0.0956-0.5938-0.51580.3123-0.1395-0.00860.30540.24390.0179-0.02680.35830.03250.258834.599523.650797.06
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain B and resid -4:21)
2X-RAY DIFFRACTION2(chain B and resid 33:48)
3X-RAY DIFFRACTION3(chain B and resid 66:103)
4X-RAY DIFFRACTION4(chain B and resid 104:132)
5X-RAY DIFFRACTION5(chain B and resid 133:185)
6X-RAY DIFFRACTION6(chain A and resid -3:47)
7X-RAY DIFFRACTION7(chain A and resid 68:125)
8X-RAY DIFFRACTION8(chain A and resid 126:148)
9X-RAY DIFFRACTION9(chain A and resid 149:168)
10X-RAY DIFFRACTION10(chain A and resid 169:184)

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