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- PDB-1qsm: Histone Acetyltransferase HPA2 from Saccharomyces Cerevisiae in C... -

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Basic information

Entry
Database: PDB / ID: 1qsm
TitleHistone Acetyltransferase HPA2 from Saccharomyces Cerevisiae in Complex with Acetyl Coenzyme A
ComponentsHPA2 HISTONE ACETYLTRANSFERASE
KeywordsTRANSFERASE / PROTEIN-ACETYL COENZYME A COMPLEX / ACETYLTRANSFERASE
Function / homology
Function and homology information


polyamine acetylation / Hpa2 acetyltransferase complex / N-acetyltransferase activity / protein acetylation / 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
ACETYL COENZYME *A / Histone acetyltransferase HPA2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsAngus-Hill, M.L. / Dutnall, R.N. / Tafrov, S.T. / Sternglanz, 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 / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9278
Polymers71,6884
Non-polymers3,2384
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: HPA2 HISTONE ACETYLTRANSFERASE
D: HPA2 HISTONE ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4634
Polymers35,8442
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-42 kcal/mol
Surface area14340 Å2
MethodPISA
3
A: HPA2 HISTONE ACETYLTRANSFERASE
B: HPA2 HISTONE ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4634
Polymers35,8442
Non-polymers1,6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-37 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.600, 184.100, 70.000
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: 17922.111 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
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, MES, CALCIUM ACETATE, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
28 %(w/v)PEG40001reservoir
30.1 MMES1reservoir
415 Mcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS / Detector: CCD / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 456328 / Num. obs: 456328 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 21
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.113 / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 37150 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Num. measured all: 456328
Reflection shell
*PLUS
Redundancy: 8.5 % / Mean I/σ(I) obs: 7.66

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Processing

Software
NameVersionClassification
SOLVEphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementRfactor Rfree error: 0.003 / Highest resolution: 2.4 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
Rfree0.244 5032 9.9 %RANDOM
Rwork0.168 ---
obs0.168 51053 71.8 %-
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.27 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5011 0 204 190 5405
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.01
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.081.5
X-RAY DIFFRACTIONx_mcangle_it4.552
X-RAY DIFFRACTIONx_scbond_it5.092
X-RAY DIFFRACTIONx_scangle_it6.962.5
LS refinement shellResolution: 2.4→2.55 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.244 0
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.01
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

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