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- PDB-1q2d: Crystal Structure of Tetrahymena GCN5 With Bound Coenzyme A and a... -

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Basic information

Entry
Database: PDB / ID: 1q2d
TitleCrystal Structure of Tetrahymena GCN5 With Bound Coenzyme A and a 19-residue p53 peptide
Components
  • 19-mer peptide fragment from p53 Tumor Suppressor
  • histone acetyltransferase GCN5
KeywordsTRANSFERASE/STRUCTURAL PROTEIN / Tetrahymena / GCN5 / Histone H4 / X-ray structure / TRANSFERASE-STRUCTURAL PROTEIN COMPLEX
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
COENZYME A / Histone acetyltransferase GCN5
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPoux, A.N. / Marmorstein, R.
CitationJournal: Biochemistry / Year: 2003
Title: Molecular basis for GCN5/PCAF histone acetyltransferase selectivity for histone and nonhistone substrates
Authors: Poux, A.N. / Marmorstein, R.
History
DepositionJul 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: histone acetyltransferase GCN5
B: 19-mer peptide fragment from p53 Tumor Suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2393
Polymers21,4722
Non-polymers7681
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-7 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.740, 64.740, 96.413
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

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Components

#1: Protein histone acetyltransferase GCN5 / E.C.2.3.1.- / HAT A1


Mass: 19344.500 Da / Num. of mol.: 1 / Fragment: Residues 49-209, catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Plasmid: PRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21
References: UniProt: Q27198, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide 19-mer peptide fragment from p53 Tumor Suppressor


Mass: 2127.330 Da / Num. of mol.: 1 / Fragment: Residues 311-329 / Source method: obtained synthetically
#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.: 62 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, Hepes, Sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9213 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 8, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9213 Å / Relative weight: 1
ReflectionResolution: 1.9→27.8 Å / Num. obs: 23773 / % possible obs: 87 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.4 Å2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QSN

1qsn


Resolution: 2.25→27.88 Å / Rfactor Rfree error: 0.018 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1103 10.1 %RANDOM
Rwork0.2469 ---
all-11565 --
obs-10902 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.0049 Å2 / ksol: 0.843632 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.937 Å2-5.774 Å20 Å2
2---3.937 Å20 Å2
3---7.873 Å2
Refine analyzeLuzzati coordinate error free: 0.57 Å
Refinement stepCycle: LAST / Resolution: 2.25→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 48 62 1498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00852
X-RAY DIFFRACTIONc_angle_deg1.5147
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.552 190 10.3 %
Rwork0.566 1656 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2COA_OLD.PARCOA_OLD.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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