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- PDB-1nfh: Structure of a Sir2 substrate, alba, reveals a mechanism for deac... -

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Basic information

Entry
Database: PDB / ID: 1nfh
TitleStructure of a Sir2 substrate, alba, reveals a mechanism for deactylation-induced enhancement of DNA-binding
Componentsconserved hypothetical protein AF1956
KeywordsGENE REGULATION / Sir2 / alba / HDAC / transcription
Function / homology
Function and homology information


chromosome condensation / chromosome / double-stranded DNA binding / RNA binding / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Alba / Alba-like domain / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA/RNA-binding protein Alba 2
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å
AuthorsZhao, K. / Chai, X. / Marmorstein, R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of a Sir2 substrate, Alba, reveals a mechanism for deacetylation-induced enhancement of DNA-binding
Authors: Zhao, K. / Chai, X. / Marmorstein, R.
History
DepositionDec 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein AF1956
B: conserved hypothetical protein AF1956


Theoretical massNumber of molelcules
Total (without water)19,8172
Polymers19,8172
Non-polymers00
Water1,53185
1
A: conserved hypothetical protein AF1956
B: conserved hypothetical protein AF1956

A: conserved hypothetical protein AF1956
B: conserved hypothetical protein AF1956


Theoretical massNumber of molelcules
Total (without water)39,6344
Polymers39,6344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_454x-1/2,-y+1/2,-z-3/41
Unit cell
Length a, b, c (Å)86.590, 86.590, 81.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein conserved hypothetical protein AF1956 / alba


Mass: 9908.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pGEX 4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O28323
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.86 Å3/Da / Density % sol: 68.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: iso-propanol, KCl, MgCl2, Na-cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
215 %isopropanol1reservoir
350 mMsodium cacodylate1reservoirpH6.0
4100 mM1reservoirKCl
525 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793, 0.9595, 0.9686
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2002
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.95951
30.96861
ReflectionResolution: 2.65→20 Å / Num. obs: 9156 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.082 / Net I/σ(I): 21.8
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 6 / Num. unique all: 899 / Rsym value: 0.272 / % possible all: 97.7
Reflection
*PLUS
% possible obs: 96.6 %
Reflection shell
*PLUS
% possible obs: 97.7 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.65→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 924 -RANDOM
Rwork0.237 ---
obs0.247 8852 95.5 %-
all-9156 --
Displacement parametersBiso mean: 48.2 Å2
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1342 0 0 85 1427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.3
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3

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