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- PDB-1mja: Crystal structure of yeast Esa1 histone acetyltransferase domain ... -

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Basic information

Entry
Database: PDB / ID: 1mja
TitleCrystal structure of yeast Esa1 histone acetyltransferase domain complexed with acetyl coenzyme A
ComponentsEsa1 protein
KeywordsTRANSFERASE / Esa1 / Histone acetyltransferase / HAT / MYST
Function / homology
Function and homology information


DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / DNA-templated transcription elongation / positive regulation of triglyceride biosynthetic process / histone H4 acetyltransferase activity ...DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / piccolo histone acetyltransferase complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / histone H4K16 acetyltransferase activity / peptide 2-hydroxyisobutyryltransferase activity / histone crotonyltransferase activity / DNA-templated transcription elongation / positive regulation of triglyceride biosynthetic process / histone H4 acetyltransferase activity / rDNA heterochromatin formation / peptide N-acetyltransferase activity / NuA4 histone acetyltransferase complex / peptide-lysine-N-acetyltransferase activity / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone 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 / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / 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 / Chromo/chromo shadow domain ...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 / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsYan, Y. / Harper, S. / Speicher, D. / Marmorstein, R.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: The catalytic mechanism of the ESA1 histone acetyltransferase involves a self-acetylated intermediate.
Authors: Yan, Y. / Harper, S. / Speicher, D.W. / Marmorstein, R.
History
DepositionAug 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esa1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1822
Polymers33,4141
Non-polymers7681
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Esa1 protein
hetero molecules

A: Esa1 protein
hetero molecules

A: Esa1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,5466
Polymers100,2433
Non-polymers2,3033
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area8090 Å2
ΔGint-12 kcal/mol
Surface area39970 Å2
MethodPISA
3
A: Esa1 protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)205,09212
Polymers200,4876
Non-polymers4,6056
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
crystal symmetry operation38_555-y+1/4,-x+1/4,-z+1/41
crystal symmetry operation42_454-x-1/4,z+1/4,y-1/41
crystal symmetry operation46_455z-1/4,-y+3/4,x+1/41
MethodPQS
Unit cell
Length a, b, c (Å)181.274, 181.274, 181.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
DetailsThe biological assembly is a monomer, which is also the asymmetric unit.

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Components

#1: Protein Esa1 protein / Esa1 histone acetyltransferase


Mass: 33414.453 Da / Num. of mol.: 1
Fragment: Histone acetyltransferase domain (Residues 160-445)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YOR244W / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(lysS) / References: UniProt: Q08649
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


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


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.71 Å3/Da / Density % sol: 66.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium cacodylate, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 mMprotein1drop
20.5 mMAc-CoA1drop
3100 mMsodium cacodylate1reservoirpH6.5
41.5-1.7 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 12, 2001 / Details: mirrors
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→20 Å / Num. all: 23988 / Num. obs: 23988 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 72.7 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 30.2
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2338 / Rsym value: 0.355 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 24067 / Num. measured all: 1744021 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Rmerge(I) obs: 0.355

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FY7

1fy7


Resolution: 2.26→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2410 -random
Rwork0.213 ---
all-23970 --
obs-23970 99.9 %-
Refinement stepCycle: LAST / Resolution: 2.26→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 48 129 2491
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.7981.5
X-RAY DIFFRACTIONc_mcangle_it2.6672
X-RAY DIFFRACTIONc_scbond_it3.2422
X-RAY DIFFRACTIONc_scangle_it4.6532.5
LS refinement shellResolution: 2.26→2.28 Å /
RfactorNum. reflection
Rfree0.239 38
Rwork0.236 -
obs-479
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2coa.par
X-RAY DIFFRACTION3water_rep.param
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.222
LS refinement shell
*PLUS
Rfactor Rfree: 0.239 / Rfactor Rwork: 0.236

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