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- PDB-1qso: Histone Acetyltransferase HPA2 from Saccharomyces Cerevisiae -

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Basic information

Entry
Database: PDB / ID: 1qso
TitleHistone Acetyltransferase HPA2 from Saccharomyces Cerevisiae
ComponentsHPA2 HISTONE ACETYLTRANSFERASE
KeywordsTRANSFERASE / TETRAMER / HISTONE ACETYLTRANSFERASE
Function / homology
Function and homology information


polyamine acetylation / Hpa2 acetyltransferase complex / N-acetyltransferase activity / histone acetyltransferase activity / histone acetyltransferase / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone acetyltransferase HPA2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsAngus-Hill, M.L. / Dutnall, R.N. / Tafrov, S.T. / Sterngalnz, R. / Ramakrishnan, V.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the histone acetyltransferase Hpa2: A tetrameric member of the Gcn5-related N-acetyltransferase superfamily.
Authors: Angus-Hill, M.L. / Dutnall, R.N. / Tafrov, S.T. / Sternglanz, R. / Ramakrishnan, V.
History
DepositionJun 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HPA2 HISTONE ACETYLTRANSFERASE
B: HPA2 HISTONE ACETYLTRANSFERASE
C: HPA2 HISTONE ACETYLTRANSFERASE
D: HPA2 HISTONE ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)70,3634
Polymers70,3634
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: HPA2 HISTONE ACETYLTRANSFERASE
B: HPA2 HISTONE ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)35,1822
Polymers35,1822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-34 kcal/mol
Surface area14520 Å2
MethodPISA
3
C: HPA2 HISTONE ACETYLTRANSFERASE
D: HPA2 HISTONE ACETYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)35,1822
Polymers35,1822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-34 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.500, 187.100, 68.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
HPA2 HISTONE ACETYLTRANSFERASE


Mass: 17590.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET13A / Production host: Escherichia coli (E. coli) / References: UniProt: Q06592, histone acetyltransferase

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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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, TRIS.CL, CALCIUM ACETATE, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
215 %PEG40001reservoir
30.1 MTris1reservoir
40.15 Mcalcium acetate1reservoir
520 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.93
DetectorType: BRANDEIS / Detector: CCD / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 168213 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 73.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 6.5
Reflection shellResolution: 2.9→3.13 Å / Redundancy: 4 % / Rmerge(I) obs: 0.231 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 21539 / Num. measured all: 168213
Reflection shell
*PLUS
Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
SOLVEphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementRfactor Rfree error: 0.005 / Highest resolution: 2.9 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.273 3516 9.9 %RANDOM
Rwork0.19 ---
obs0.19 35558 87.3 %-
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.35 Å
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4980 0 0 0 4980
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.02
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.951.5
X-RAY DIFFRACTIONx_mcangle_it4.652
X-RAY DIFFRACTIONx_scbond_it4.62
X-RAY DIFFRACTIONx_scangle_it6.452.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 430 9.6 %
Rwork0.245 4029 -
obs--65.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.02
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.296 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.245

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