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- PDB-1fy7: CRYSTAL STRUCTURE OF YEAST ESA1 HISTONE ACETYLTRANSFERASE DOMAIN ... -

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Basic information

Entry
Database: PDB / ID: 1fy7
TitleCRYSTAL STRUCTURE OF YEAST ESA1 HISTONE ACETYLTRANSFERASE DOMAIN COMPLEXED WITH COENZYME A
ComponentsESA1 HISTONE ACETYLTRANSFERASE
KeywordsTRANSFERASE / HISTONE ACETYLTRANSFERASE / coenzyme A
Function / homology
Function and homology information


DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / positive regulation of triglyceride biosynthetic process / DNA-templated transcription elongation / histone H4 acetyltransferase activity / rDNA heterochromatin formation / protein N-acetyltransferase activity ...DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / positive regulation of triglyceride biosynthetic process / DNA-templated transcription elongation / histone H4 acetyltransferase activity / rDNA heterochromatin formation / protein N-acetyltransferase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein-lysine-acetyltransferase activity / NuA4 histone acetyltransferase complex / histone acetyltransferase activity / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / nucleosome / regulation of cell cycle / DNA repair / DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleus
Similarity search - Function
N-acetyl transferase-like / : / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Wheat Germ Agglutinin (Isolectin 2); domain 1 ...N-acetyl transferase-like / : / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Histone acetyltransferase ESA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsYan, Y. / Barlev, N.A. / Haley, R.H. / Berger, S.L. / Marmorstein, R.
CitationJournal: Mol.Cell / Year: 2000
Title: Crystal structure of yeast Esa1 suggests a unified mechanism for catalysis and substrate binding by histone acetyltransferases.
Authors: Yan, Y. / Barlev, N.A. / Haley, R.H. / Berger, S.L. / Marmorstein, R.
History
DepositionSep 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ESA1 HISTONE ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1633
Polymers33,3721
Non-polymers7912
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ESA1 HISTONE ACETYLTRANSFERASE
hetero molecules

A: ESA1 HISTONE ACETYLTRANSFERASE
hetero molecules

A: ESA1 HISTONE ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4899
Polymers100,1173
Non-polymers2,3726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area8760 Å2
ΔGint-53 kcal/mol
Surface area39680 Å2
MethodPISA
3
A: ESA1 HISTONE ACETYLTRANSFERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)204,97818
Polymers200,2346
Non-polymers4,74312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
crystal symmetry operation37_544y+1/4,x-1/4,-z-1/41
crystal symmetry operation42_554-x+3/4,z+1/4,y-1/41
crystal symmetry operation48_555-z+1/4,-y+1/4,-x+1/41
MethodPQS
Unit cell
Length a, b, c (Å)181.500, 181.500, 181.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Cell settingtetragonal
Space group name H-MI4132
DetailsThe biological assembly is a monomer of yeast Esa1 HAT domain bound to coenzyme-A.

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Components

#1: Protein ESA1 HISTONE ACETYLTRANSFERASE / ESA1 HAT / ESA1 PROTEIN / ESA1P


Mass: 33372.414 Da / Num. of mol.: 1 / Fragment: ACETYLTRANSFERASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PRSETA / Production host: Escherichia coli (E. coli) / References: UniProt: Q08649
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: amonium phosphate, cacodylate,, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.5 mMCoA1drop
3100 mMsodium cacodylate1reservoir
41.7 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 26, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 34558 / Num. obs: 34558 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 35.9 % / Biso Wilson estimate: 29.13 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 48.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.272 / Num. unique all: 3413 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 1241495
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: CNS Library / Details: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3397 9.9 %RANDOM
Rwork0.219 ---
all0.217 34558 --
obs0.216 34295 99.3 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 49 178 2538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.222

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