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- PDB-4yrh: p21 isoform of MEC-17 from Danio Rerio -

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Basic information

Entry
Database: PDB / ID: 4yrh
Titlep21 isoform of MEC-17 from Danio Rerio
ComponentsAlpha-tubulin N-acetyltransferase 1
KeywordsTRANSFERASE / Acetyltransferase / acetylation / complex
Function / homology
Function and homology information


alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / alpha-tubulin acetylation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / neuron development / regulation of microtubule cytoskeleton organization / clathrin-coated pit / spindle / microtubule / axon ...alpha-tubulin N-acetyltransferase / tubulin N-acetyltransferase activity / alpha-tubulin acetylation / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / neuron development / regulation of microtubule cytoskeleton organization / clathrin-coated pit / 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 / Alpha-tubulin N-acetyltransferase 1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.861 Å
AuthorsXue, T.
Funding support China, 1items
OrganizationGrant numberCountry
Tianjin Natural Science Foundationgrant 14JCQNJC09300 China
CitationJournal: To Be Published
Title: Structure of DrMEC-17 residue 2-185 at 2.85 Angstroms resolution
Authors: Xue, T.
History
DepositionMar 15, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-tubulin N-acetyltransferase 1
B: Alpha-tubulin N-acetyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8676
Polymers41,7712
Non-polymers2,0964
Water1448
1
A: Alpha-tubulin N-acetyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9333
Polymers20,8861
Non-polymers1,0482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-2 kcal/mol
Surface area10040 Å2
MethodPISA
2
B: Alpha-tubulin N-acetyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9333
Polymers20,8861
Non-polymers1,0482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-4 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.374, 66.299, 75.841
Angle α, β, γ (deg.)90.00, 103.84, 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: 20885.523 Da / Num. of mol.: 2 / Fragment: UNP residues 2-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: atat1, mec17 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6PH17, alpha-tubulin N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.2 Å3/Da / Density % sol: 70.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG3350, 0.1M HEPES, 0.2M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 32007 / % possible obs: 98.9 % / Redundancy: 7 % / Net I/σ(I): 18.57

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data processing
HKL-2000data scaling
Cootmodel building
RefinementResolution: 2.861→49.272 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.7 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2557 1652 10.03 %
Rwork0.2176 --
obs0.2214 16465 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.861→49.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 132 8 2923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053025
X-RAY DIFFRACTIONf_angle_d0.9254107
X-RAY DIFFRACTIONf_dihedral_angle_d16.7481195
X-RAY DIFFRACTIONf_chiral_restr0.036432
X-RAY DIFFRACTIONf_plane_restr0.003508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8609-2.94510.32151320.29961111X-RAY DIFFRACTION91
2.9451-3.04010.3381290.26941235X-RAY DIFFRACTION97
3.0401-3.14880.32781350.26251224X-RAY DIFFRACTION98
3.1488-3.27480.35121380.24711227X-RAY DIFFRACTION99
3.2748-3.42380.32141370.25911215X-RAY DIFFRACTION98
3.4238-3.60430.27531410.23721247X-RAY DIFFRACTION99
3.6043-3.830.27041390.21131238X-RAY DIFFRACTION99
3.83-4.12560.22211360.17861258X-RAY DIFFRACTION100
4.1256-4.54050.19421400.16981257X-RAY DIFFRACTION100
4.5405-5.19690.19041400.18731250X-RAY DIFFRACTION100
5.1969-6.54510.23561430.2281261X-RAY DIFFRACTION100
6.5451-49.2790.26671420.2211290X-RAY DIFFRACTION98

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