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- PDB-1qsn: CRYSTAL STRUCTURE OF TETRAHYMENA GCN5 WITH BOUND COENZYME A AND H... -

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Basic information

Entry
Database: PDB / ID: 1qsn
TitleCRYSTAL STRUCTURE OF TETRAHYMENA GCN5 WITH BOUND COENZYME A AND HISTONE H3 PEPTIDE
Components
  • HISTONE H3
  • TGCN5 HISTONE ACETYL TRANSFERASE
KeywordsTRANSFERASE / HISTONE ACETYLTRANSFERASE / GCN5-RELATED N-ACETYLTRANSFERASE / COA-BINDING PROTEIN / TERNARY COMPLEX
Function / homology
Function and homology information


sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / replication fork protection complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / CENP-A containing nucleosome / histone acetyltransferase activity / histone acetyltransferase ...sexual sporulation resulting in formation of a cellular spore / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / replication fork protection complex / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / CENP-A containing nucleosome / histone acetyltransferase activity / histone acetyltransferase / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / nucleus
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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Histone H3 / Histone acetyltransferase GCN5
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsRojas, J.R. / Trievel, R.C. / Zhou, J. / Mo, Y. / Li, X. / Berger, S.L. / David Allis, C. / Marmorstein, R.
CitationJournal: Nature / Year: 1999
Title: Structure of Tetrahymena GCN5 bound to coenzyme A and a histone H3 peptide.
Authors: Rojas, J.R. / Trievel, R.C. / Zhou, J. / Mo, Y. / Li, X. / Berger, S.L. / Allis, C.D. / Marmorstein, R.
History
DepositionJun 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: TGCN5 HISTONE ACETYL TRANSFERASE
B: HISTONE H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2733
Polymers20,5062
Non-polymers7681
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-5 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.090, 65.090, 96.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TGCN5 HISTONE ACETYL TRANSFERASE


Mass: 19344.500 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Plasmid: PRSET A / Production host: Escherichia coli (E. coli)
References: UniProt: Q27198, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide HISTONE H3 /


Mass: 1161.355 Da / Num. of mol.: 1 / Fragment: 11 MER PEPTIDE (RESIDUES 9 - 19) / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61830
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


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


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: TRIS, AMMONIUM SULFATE, MANGANESE CHLORIDE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 mg/mlprotein1drop
21 mMCoA1drop
31.5 mMpeptide1drop
41.6 Mammonium sulfate1reservoir
550 mMTris1reservoir
610 mM1reservoirMnCl2

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.917
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 13391 / Num. obs: 12960 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 33.3
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.066 / % possible all: 77.9
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 15.1 % / Num. measured all: 201683
Reflection shell
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 2.21 Å / Redundancy: 5.7 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→30 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: USED MAXIMUM LIKELIHOOD ALGORITHM
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1300 -RANDOM
Rwork0.239 ---
obs0.239 12960 96.4 %-
all-13064 --
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 48 122 1602
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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