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- PDB-2qqg: Hst2 bound to ADP-HPD, acetyllated histone H4 and nicotinamide -

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Basic information

Entry
Database: PDB / ID: 2qqg
TitleHst2 bound to ADP-HPD, acetyllated histone H4 and nicotinamide
Components
  • Histone H4
  • NAD-dependent deacetylase HST2
KeywordsHYDROLASE / Hst2 / Sir2 / histone deacetylase / Metal-binding / NAD / Nucleus / Repressor / Transcription / Transcription regulation / Zinc
Function / homology
Function and homology information


negative regulation of mitotic recombination / HDMs demethylate histones / HATs acetylate histones / NAD-dependent histone H4K16 deacetylase activity / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity ...negative regulation of mitotic recombination / HDMs demethylate histones / HATs acetylate histones / NAD-dependent histone H4K16 deacetylase activity / Condensation of Prophase Chromosomes / RNA polymerase I upstream activating factor complex / SUMOylation of chromatin organization proteins / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / replication fork protection complex / RMTs methylate histone arginines / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / NAD+ binding / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / transferase activity / protein heterodimerization activity / regulation of DNA-templated transcription / DNA 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 / DHS-like NAD/FAD-binding domain superfamily ...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 / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A1R / NICOTINAMIDE / Histone H4 / NAD-dependent protein deacetylase HST2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMarmorstein, R. / Sanders, B. / Zhao, K. / Slama, J.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural basis for nicotinamide inhibition and base exchange in sir2 enzymes.
Authors: Sanders, B.D. / Zhao, K. / Slama, J.T. / Marmorstein, R.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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_conn / struct_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent deacetylase HST2
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8355
Polymers36,1052
Non-polymers7303
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
2
A: NAD-dependent deacetylase HST2
B: Histone H4
hetero molecules

A: NAD-dependent deacetylase HST2
B: Histone H4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,67110
Polymers72,2114
Non-polymers1,4606
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area5240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.940, 105.940, 67.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein NAD-dependent deacetylase HST2 / Homologous to SIR2 protein 2


Mass: 34794.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HST2 / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli) / Strain (production host): SL21 gold
References: UniProt: P53686, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Histone H4 /


Mass: 1310.615 Da / Num. of mol.: 1 / Fragment: sequence database residues 13-23 / Source method: obtained synthetically
Details: The H4 peptide was chemically synthesized using standard solid phase synthesis chemistry. The peptide is naturally found in Saccharomyces cerevisiae.
References: UniProt: P02309

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Non-polymers , 4 types, 119 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1R / 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE


Mass: 542.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N6O12P2
#5: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.12 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 298 K / pH: 5.6
Details: 2.0 M Ammonium Sulfate, 100 mM Na citrate, pH 5.6, 200 mM K/Na tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.60

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 16, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 27580 / % possible obs: 99.9 % / Observed criterion σ(I): 6.1 / Redundancy: 6.1 % / Rmerge(I) obs: 0.111 / Rsym value: 0.117 / Net I/σ(I): 13.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.32 / % possible all: 99.6

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Phasing

Phasing MRRfactor: 0.389 / Cor.coef. Fo:Fc: 0.658 / Cor.coef. Io to Ic: 0.404
Highest resolutionLowest resolution
Rotation3 Å91.287 Å
Translation3 Å91.287 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SZD

1szd


Resolution: 2.05→28.34 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.245 2636 8.9 %
Rwork0.218 --
obs0.218 26344 88.8 %
Solvent computationBsol: 59.07 Å2
Displacement parametersBiso mean: 36.86 Å2
Baniso -1Baniso -2Baniso -3
1-7.01 Å23.07 Å20 Å2
2--7.01 Å20 Å2
3----14.02 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 45 116 2527
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION3HPD_NIC.PARAM
X-RAY DIFFRACTION4CNS_TOPPAR:WATER_REP.PARAM

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