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- PDB-1qst: CRYSTAL STRUCTURE OF TETRAHYMENA GCN5 -

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Basic information

Entry
Database: PDB / ID: 1qst
TitleCRYSTAL STRUCTURE OF TETRAHYMENA GCN5
ComponentsTGCN5 HISTONE ACETYL TRANSFERASE
KeywordsTRANSFERASE / HISTONE ACETYLTRANSFERASE / GCN5-RELATED N-ACETYLTRANSFERASE / COA BINDING PROTEIN
Function / homology
Function and homology information


histone acetyltransferase activity / histone acetyltransferase / 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 / 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 speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 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 23, 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 2.0Feb 14, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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: TGCN5 HISTONE ACETYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3692
Polymers19,1301
Non-polymers2381
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.10, 64.10, 97.80
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: 19130.256 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: LITHIUM SULFATE, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.5 mg/mlprotein1drop
20.5 M1dropLi2SO4
340 mMHEPES1drop
41.25 M1reservoirLi2SO4
5100 mMHEPES1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONCHESS F210.984
SYNCHROTRONNSLS X8C21.0093
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 29, 1998
MAR scanner 345 mm plate2IMAGE PLATEJul 11, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9841
21.00931
ReflectionResolution: 1.7→20 Å / Num. all: 25427 / Num. obs: 25409 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 19.6 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 9.4
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.149 / % possible all: 86.3
Reflection
*PLUS
Num. obs: 25427 / Num. measured all: 497452

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.7→8 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2489 -RANDOM
Rwork0.244 ---
obs0.244 25165 99.1 %-
all-25403 --
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1345 0 15 96 1456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.292
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

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