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- PDB-2od2: Crystal Structure of yHst2 I117F mutant bound to carba-NAD+ and a... -

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Basic information

Entry
Database: PDB / ID: 2od2
TitleCrystal Structure of yHst2 I117F mutant bound to carba-NAD+ and an acetylated H4 peptide
Components
  • Acetylated H4 peptide
  • NAD-dependent deacetylase HST2
KeywordsHYDROLASE / Zn binding protein / Rossmann fold
Function / homology
Function and homology information


Transcriptional activation of mitochondrial biogenesis / negative regulation of mitotic recombination / NAD-dependent histone H4K16 deacetylase activity / rDNA heterochromatin formation / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / NAD+ binding / transferase activity / nucleus / metal ion binding / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent protein deacetylase HST2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSanders, B.D.
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
DepositionDec 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 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 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,5368
Polymers36,4402
Non-polymers1,0966
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-13 kcal/mol
Surface area13980 Å2
MethodPISA
2
A: NAD-dependent deacetylase HST2
B: Acetylated H4 peptide
hetero molecules

A: NAD-dependent deacetylase HST2
B: Acetylated H4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,07216
Polymers72,8804
Non-polymers2,19212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area9160 Å2
ΔGint-40 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.639, 106.639, 67.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological unit is a trimer generated by the monomer in the assymetric unit.

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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: 34828.844 Da / Num. of mol.: 1 / Fragment: Hst2 catalytic core domain, residues 1-294 / Mutation: I117F
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): DE3 BL-21 gold
References: UniProt: P53686, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Acetylated H4 peptide


Mass: 1610.925 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Homo sapiens (Humans)

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Non-polymers , 4 types, 172 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CNA / CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 662.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H30N7O13P2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.0 M Ammonium Sulfate, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 53931 / Num. obs: 31864 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.047 / Χ2: 1 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.218 / Num. unique all: 3032 / Χ2: 0.971 / % possible all: 86.4

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Phasing

Phasing MRRfactor: 0.401 / Cor.coef. Fo:Fc: 0.588 / Cor.coef. Io to Ic: 0.158
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 collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry ISZC

Resolution: 2→41.89 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2597 8.6 %random
Rwork0.225 ---
all0.129 53931 --
obs0.114 26083 86 %-
Solvent computationBsol: 61.735 Å2
Displacement parametersBiso mean: 41.517 Å2
Baniso -1Baniso -2Baniso -3
1-10.474 Å24.866 Å20 Å2
2--10.474 Å20 Å2
3----20.949 Å2
Refinement stepCycle: LAST / Resolution: 2→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 69 166 2602
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 2→6 Å
RfactorNum. reflection% reflection
Rfree0.233 2597 -
Rwork0.225 --
obs-26083 86 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3carbagol.param
X-RAY DIFFRACTION4water_rep.param

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