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- PDB-1ygh: HAT DOMAIN OF GCN5 FROM SACCHAROMYCES CEREVISIAE -

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Basic information

Entry
Database: PDB / ID: 1ygh
TitleHAT DOMAIN OF GCN5 FROM SACCHAROMYCES CEREVISIAE
ComponentsPROTEIN (TRANSCRIPTIONAL ACTIVATOR GCN5)
KeywordsGENE REGULATION / TRANSCRIPTIONAL REGULATION / HISTONE ACETYLATION / N-ACETYLTRANSFERASE / GCN5 RELATED N-ACETYLTRANSFERASE FAMILY
Function / homology
Function and homology information


ADA complex / histone crotonyltransferase activity / histone H3 acetyltransferase activity / SLIK (SAGA-like) complex / SAGA complex / peptide-lysine-N-acetyltransferase activity / Estrogen-dependent gene expression / chromosome, centromeric region / histone acetyltransferase complex / histone acetyltransferase activity ...ADA complex / histone crotonyltransferase activity / histone H3 acetyltransferase activity / SLIK (SAGA-like) complex / SAGA complex / peptide-lysine-N-acetyltransferase activity / Estrogen-dependent gene expression / chromosome, centromeric region / histone acetyltransferase complex / histone acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / histone acetyltransferase / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / chromatin organization / chromatin remodeling / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone acetyltransferase GCN5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTrievel, R.C. / Rojas, J.R. / Sterner, D.E. / Venkataramani, R. / Wang, L. / Zhou, J. / Allis, C.D. / Berger, S.L. / Marmorstein, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure and mechanism of histone acetylation of the yeast GCN5 transcriptional coactivator.
Authors: Trievel, R.C. / Rojas, J.R. / Sterner, D.E. / Venkataramani, R.N. / Wang, L. / Zhou, J. / Allis, C.D. / Berger, S.L. / Marmorstein, R.
History
DepositionMay 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 25, 2019Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.4Dec 27, 2023Group: 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (TRANSCRIPTIONAL ACTIVATOR GCN5)
B: PROTEIN (TRANSCRIPTIONAL ACTIVATOR GCN5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6814
Polymers38,4972
Non-polymers1842
Water3,891216
1
A: PROTEIN (TRANSCRIPTIONAL ACTIVATOR GCN5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3412
Polymers19,2481
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN (TRANSCRIPTIONAL ACTIVATOR GCN5)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3412
Polymers19,2481
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.040, 66.510, 80.190
Angle α, β, γ (deg.)90.00, 97.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999966, 0.005455, 0.0062), (0.005633, -0.999561, -0.029096), (0.006039, 0.02913, -0.999557)
Vector: 34.79428, 17.3449, 39.76963)

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Components

#1: Protein PROTEIN (TRANSCRIPTIONAL ACTIVATOR GCN5) / ADA4


Mass: 19248.455 Da / Num. of mol.: 2 / Fragment: HISTONE ACETYLTRANSFERASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Cellular location: NUCLEAR / Gene: GCN5 / Plasmid: PRSET / Species (production host): Escherichia coli / Gene (production host): GCN5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03330, histone acetyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growpH: 6
Details: 400 MM AMMONIUM SULFATE, 20% - 25% PEG 8000, pH 6.0
Temp details: 277
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
2400 mMammonium sulfate1reservoir
320-25 %PEG80001reservoir

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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: Oct 1, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 31832 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 18.6 Å2 / Rsym value: 0.03 / Net I/σ(I): 23.6
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 13 / Rsym value: 0.088 / % possible all: 98
Reflection
*PLUS
Num. measured all: 181066 / Rmerge(I) obs: 0.03

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TETRAHYMENA THERMOPHILA GCN5 HAT DOMAIN

Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3167 10 %RANDOM
Rwork0.195 ---
obs0.195 31686 96.4 %-
Displacement parametersBiso mean: 16.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 12 216 2930
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.269 410 11.5 %
Rwork0.261 3554 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2GOL_XPLOR_PARTOPH19.SOL
X-RAY DIFFRACTION3GOL_XPLOR_TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.9 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.269 / Rfactor Rwork: 0.261

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