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- PDB-2h2i: The Structural basis of Sirtuin Substrate Affinity -

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Basic information

Entry
Database: PDB / ID: 2h2i
TitleThe Structural basis of Sirtuin Substrate Affinity
ComponentsNAD-dependent deacetylase
KeywordsHYDROLASE / Sir2Tm-PPG
Function / homology
Function and homology information


protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / histone deacetylase activity, NAD-dependent / NAD+ binding / zinc ion binding / cytoplasm
Similarity search - Function
Sirtuin, class U / 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 U / 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
Chem-ZPG / NAD-dependent protein deacetylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsCosgrove, M.S. / Wolberger, C.
CitationJournal: Biochemistry / Year: 2006
Title: The structural basis of sirtuin substrate affinity
Authors: Cosgrove, M.S. / Bever, K. / Avalos, J.L. / Muhammad, S. / Zhang, X. / Wolberger, C.
History
DepositionMay 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 27, 2012Group: Structure summary
Revision 1.4Aug 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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: NAD-dependent deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0603
Polymers27,5701
Non-polymers4902
Water3,747208
1
A: NAD-dependent deacetylase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)224,47824
Polymers220,5588
Non-polymers3,92016
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_556-y,-x,-z+11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Unit cell
Length a, b, c (Å)133.107, 133.107, 133.107
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-1119-

HOH

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Components

#1: Protein NAD-dependent deacetylase / Regulatory protein SIR2 homolog


Mass: 27569.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: npdA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WYW0, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ZPG / (2S,5R,8R,11S,14S,17S,21R)-5,8,11,14,17-PENTAMETHYL-4,7,10,13,16,19-HEXAOXADOCOSANE-2,21-DIOL


Mass: 424.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 3.56 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.5M (NH4)2SO4, 4% PPG, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Dec 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 37913 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 18 % / Rmerge(I) obs: 0.078
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 10 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ADSCdata collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1ICI

1ici


Resolution: 1.8→129.1 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.835 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21253 1889 5 %RANDOM
Rwork0.18633 ---
all0.03 3 --
obs0.18767 35987 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.136 Å2
Refinement stepCycle: LAST / Resolution: 1.8→129.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 30 208 2159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222002
X-RAY DIFFRACTIONr_bond_other_d0.0020.021887
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9942704
X-RAY DIFFRACTIONr_angle_other_deg0.9134402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975243
X-RAY DIFFRACTIONr_chiral_restr0.1070.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022161
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02383
X-RAY DIFFRACTIONr_nbd_refined0.2180.2411
X-RAY DIFFRACTIONr_nbd_other0.2450.22194
X-RAY DIFFRACTIONr_nbtor_other0.0870.21205
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2131
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.350.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.217
X-RAY DIFFRACTIONr_mcbond_it1.091.51219
X-RAY DIFFRACTIONr_mcangle_it1.99221983
X-RAY DIFFRACTIONr_scbond_it3.2773783
X-RAY DIFFRACTIONr_scangle_it5.3024.5721
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 136
Rwork0.239 2611

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