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- PDB-1q17: Structure of the yeast Hst2 protein deacetylase in ternary comple... -

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Basic information

Entry
Database: PDB / ID: 1q17
TitleStructure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide
ComponentsHST2 protein
KeywordsHYDROLASE / histone deacetylase
Function / homology
Function and homology information


Transcriptional activation of mitochondrial biogenesis / negative regulation of mitotic recombination / histone H4K16 deacetylase activity, NAD-dependent / protein acetyllysine N-acetyltransferase / rDNA heterochromatin formation / histone deacetylase activity, NAD-dependent / NAD+ binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain ...Sirtuin, class I / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5-DIPHOSPHORIBOSE / NAD-dependent protein deacetylase HST2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhao, K. / Chai, X. / Marmorstein, R.
Citation
Journal: Structure / Year: 2003
Title: Structure of the Yeast Hst2 Protein Deacetylase in Ternary Complex with 2'-O-Acetyl ADP Ribose and Histone Peptide.
Authors: Zhao, K. / Chai, X. / Marmorstein, R.
#1: Journal: Nat.Struct.Biol. / Year: 2003
Title: Structure and autoregulation of the yeast Hst2 homolog of Sir2
Authors: Zhao, K. / Chai, X. / Clements, A. / Marmorstein, R.
History
DepositionJul 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 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: HST2 protein
B: HST2 protein
C: HST2 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,44513
Polymers101,4293
Non-polymers2,01610
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-95 kcal/mol
Surface area38190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.159, 109.682, 85.825
Angle α, β, γ (deg.)90.00, 104.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1507-

HOH

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Components

#1: Protein HST2 protein / Homologous to SIR2 protein 2


Mass: 33809.730 Da / Num. of mol.: 3 / Fragment: protein deacetylase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HST2 OR YPL015C OR LPA2C / Production host: Escherichia coli (E. coli) / References: UniProt: P53686
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.28 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: (NH4)2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
21.2-1.4 Mammonium sulfate1reservoir
350 mMHEPES1reservoirpH7.0
410 mM1reservoirMgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2003
RadiationMonochromator: 0.9 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 35492 / Num. obs: 34976 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 10.9 / Num. unique all: 3602 / Rsym value: 0.207 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 35492
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q14

1q14


Resolution: 2.7→28.88 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 243397.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3489 10 %RANDOM
Rwork0.186 ---
all0.217 35492 --
obs0.186 34976 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.3895 Å2 / ksol: 0.328581 e/Å3
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.97 Å20 Å28.27 Å2
2--5.01 Å20 Å2
3----2.04 Å2
Refine analyzeLuzzati coordinate error free: 0.4 Å / Luzzati sigma a free: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.7→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6984 0 115 162 7261
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.751.5
X-RAY DIFFRACTIONc_mcangle_it5.632
X-RAY DIFFRACTIONc_scbond_it6.232
X-RAY DIFFRACTIONc_scangle_it8.572.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 554 9.8 %
Rwork0.259 5086 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4ADR_M
Refinement
*PLUS
Highest resolution: 2.7 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor Rfree: 0.335 / Rfactor Rwork: 0.265

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