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- PDB-1mj9: Crystal structure of yeast Esa1(C304S) mutant complexed with Coen... -

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Basic information

Entry
Database: PDB / ID: 1mj9
TitleCrystal structure of yeast Esa1(C304S) mutant complexed with Coenzyme A
ComponentsESA1 PROTEIN
KeywordsTRANSFERASE / Esa1 / HAT / Histone acetyltransferase / MYST
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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks ...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 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / protein-lysine-acetyltransferase activity / NuA4 histone acetyltransferase complex / Estrogen-dependent gene expression / positive regulation of macroautophagy / histone acetyltransferase activity / histone acetyltransferase / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESA1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1473
Polymers33,3561
Non-polymers7912
Water1,31573
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)102,4419
Polymers100,0693
Non-polymers2,3726
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 area9060 Å2
ΔGint-66 kcal/mol
Surface area39730 Å2
MethodPISA
3
A: ESA1 PROTEIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)204,88118
Polymers200,1386
Non-polymers4,74312
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)181.301, 181.301, 181.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein ESA1 PROTEIN / ESA1 HISTONE ACETYLTRANSFERASE


Mass: 33356.352 Da / Num. of mol.: 1
Fragment: HISTONE ACETYLTRANSFERASE DOMAIN (Residues 160-445)
Mutation: C304S
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-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.: 73 / 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: 3.72 Å3/Da / Density % sol: 66.94 %
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 mMCoA1drop
3100 mMsodium cacodylate1reservoirpH6.5
41.5-1.7 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 28, 2001 / Details: mirrors
RadiationMonochromator: silicon and germanium crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 17817 / Num. obs: 17817 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 25.6 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 28.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 7 / Num. unique all: 1743 / Rsym value: 0.316 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 17931 / Num. measured all: 456785 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
Rmerge(I) obs: 0.316

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1FY7

1fy7


Resolution: 2.5→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
Rfree0.255 1753 -random
Rwork0.232 ---
all-17806 --
obs-17806 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 49 73 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d1.22
X-RAY DIFFRACTIONc_angle_deg2.06
X-RAY DIFFRACTIONc_mcbond_it1.2241.5
X-RAY DIFFRACTIONc_mcangle_it1.9942
X-RAY DIFFRACTIONc_scbond_it2.0632
X-RAY DIFFRACTIONc_scangle_it2.9942.5
LS refinement shellResolution: 2.5→2.52 Å /
RfactorNum. reflection
Rfree0.327 44
Rwork0.248 -
obs-491
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2coa.par
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4water_rep.param
Refinement
*PLUS
Highest resolution: 2.5 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.222
LS refinement shell
*PLUS
Rfactor Rfree: 0.327 / Rfactor Rwork: 0.248

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