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- PDB-4if5: Structure of human Mec17 -

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Basic information

Entry
Database: PDB / ID: 4if5
TitleStructure of human Mec17
ComponentsAlpha-tubulin N-acetyltransferase
KeywordsTRANSFERASE / Acetyltransferase
Function / homology
Function and homology information


alpha-tubulin acetylation / alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / 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 acetylation / alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / 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
ACETYL COENZYME *A / Alpha-tubulin N-acetyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsDavenport, A.M. / Collins, L. / Minor, P. / Sternberg, P. / Hoelz, A.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural and Functional Characterization of the alpha-Tubulin Acetyltransferase MEC-17.
Authors: Davenport, A.M. / Collins, L.N. / Chiu, H. / Minor, P.J. / Sternberg, P.W. / Hoelz, A.
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Oct 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,4883
Polymers22,6431
Non-polymers8452
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.747, 122.297, 37.541
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21A-465-

HOH

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Components

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


Mass: 22643.320 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: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris, 200 mM NaCl, 24 % PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 21804 / Biso Wilson estimate: 23.54 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8305 / SU ML: 0.21 / σ(F): 0 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 3500 9.39 %RANDOM
Rwork0.1781 ---
obs0.1816 21804 91.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.255 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 90.37 Å2 / Biso mean: 36.2284 Å2 / Biso min: 12.13 Å2
Baniso -1Baniso -2Baniso -3
1-12.8672 Å2-0 Å2-0 Å2
2---9.3322 Å20 Å2
3----3.535 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 52 207 1812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061659
X-RAY DIFFRACTIONf_angle_d1.1072253
X-RAY DIFFRACTIONf_chiral_restr0.071242
X-RAY DIFFRACTIONf_plane_restr0.005290
X-RAY DIFFRACTIONf_dihedral_angle_d15.555645
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72720.3882850.298986995460
1.7272-1.75190.3054960.30221062115870
1.7519-1.77810.29371190.27921090120976
1.7781-1.80580.30431310.26421170130179
1.8058-1.83550.34611170.22751226134384
1.8355-1.86710.26211460.23371327147387
1.8671-1.90110.24491350.21651285142089
1.9011-1.93760.26181450.20711322146791
1.9376-1.97720.22471450.20411368151392
1.9772-2.02020.22271400.17931342148294
2.0202-2.06710.25731400.18211435157596
2.0671-2.11880.18641460.17951398154497
2.1188-2.17610.21571460.16741456160297
2.1761-2.24020.21551530.16631442159598
2.2402-2.31250.1751440.16181437158197
2.3125-2.39510.23961460.18781417156398
2.3951-2.4910.23081490.17791453160298
2.491-2.60430.21271520.17461448160099
2.6043-2.74160.25291440.18631457160199
2.7416-2.91330.23621510.19361477162899
2.9133-3.13820.24361550.18891469162499
3.1382-3.45380.17551490.16991463161299
3.4538-3.95320.19941530.148114521605100
3.9532-4.9790.18081510.139814581609100
4.979-39.51920.18561620.18961465162799

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