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- PDB-1ici: CRYSTAL STRUCTURE OF A SIR2 HOMOLOG-NAD COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ici
TitleCRYSTAL STRUCTURE OF A SIR2 HOMOLOG-NAD COMPLEX
ComponentsTRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
KeywordsTRANSCRIPTION / Rossmann fold / Zinc ribbon / protein deacetylase / NAD-binding
Function / homology
Function and homology information


protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD+ binding / transferase activity / zinc ion binding / cytoplasm
Similarity search - Function
Sirtuin, class III / 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 III / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD-dependent protein deacylase 1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMin, J. / Landry, J. / Sternglanz, R. / Xu, R.-M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Crystal structure of a SIR2 homolog-NAD complex.
Authors: Min, J. / Landry, J. / Sternglanz, R. / Xu, R.M.
History
DepositionApr 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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.pdbx_dist_value / _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_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: TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
B: TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3316
Polymers56,8732
Non-polymers1,4584
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
hetero molecules

A: TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3316
Polymers56,8732
Non-polymers1,4584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5120 Å2
ΔGint-34 kcal/mol
Surface area23080 Å2
MethodPISA, PQS
3
B: TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
hetero molecules

B: TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3316
Polymers56,8732
Non-polymers1,4584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
MethodPQS
Unit cell
Length a, b, c (Å)65.410, 94.540, 93.780
Angle α, β, γ (deg.)90.00, 95.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY


Mass: 28436.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF1676 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 BLUE / References: UniProt: O28597
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 10000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
25 mMTris-HCl1drop
3200 mM1dropNaCl
40.1 %beta-mercaptoethanol1drop
51 mMEDTA1drop
66 mMNAD1drop
7100 mMMES1reservoir
812 %PEG100001reservoir
91 mMcetyltrimethylammonium bromide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jan 1, 2000 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 30346 / Num. obs: 30346 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.199 / % possible all: 58.2
Reflection
*PLUS
Num. measured all: 85113
Reflection shell
*PLUS
% possible obs: 58.2 %

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Processing

Software
NameClassification
PHASESphasing
CNSrefinement
MADNESSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.249 2431 Random
Rwork0.199 --
all0.203 30346 -
obs0.203 30208 -
Refine analyze
FreeObs
Luzzati coordinate error0.2547 Å0.326 Å
Luzzati d res low-40 Å
Luzzati sigma a0.2016 Å0.2517 Å
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 90 261 4249
LS refinement shellResolution: 2.1→2.2 Å
RfactorNum. reflection% reflection
Rfree0.315 215 -
Rwork0.269 --
obs-2798 58.2 %
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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