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- PDB-1h0y: Structure of Alba: an archaeal chromatin protein modulated by ace... -

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Basic information

Entry
Database: PDB / ID: 1h0y
TitleStructure of Alba: an archaeal chromatin protein modulated by acetylation
ComponentsDNA BINDING PROTEIN SSO10B
KeywordsDNA BINDING / ARCHAEA / CHROMATIN / ALBA / ACETYLATION
Function / homology
Function and homology information


nuclease activity / chromosome condensation / chromosome / double-stranded DNA binding / Hydrolases; Acting on ester bonds / RNA binding / identical protein 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 1 / DNA/RNA-binding protein Alba 1
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWardleworth, B.N. / Russell, R.J.M. / Bell, S.D. / Taylor, G.L. / White, M.F.
Citation
Journal: Embo J. / Year: 2002
Title: Structure of Alba: An Archaeal Chromatin Protein Modulated by Acetylation
Authors: Wardleworth, B.N. / Russell, R.J.M. / Bell, S.D. / Taylor, G.L. / White, M.F.
#1: Journal: Science / Year: 2002
Title: The Interaction of Alba, a Conserved Archaeal Chromatin Protein, with Sir2 and its Regulation by Acetylation
Authors: Bell, S.D. / Botting, C.H. / Wardleworth, B.N. / Jackson, S.P. / White, M.F.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Preliminary Crystallographic Studies of the Double-Stranded DNA Binding Protein Sso10B from Sulfolobus Solfataricus
Authors: Wardleworth, B.N. / Russell, R.J.M. / White, M.F. / Taylor, G.L.
History
DepositionJul 1, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA BINDING PROTEIN SSO10B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0872
Polymers10,9911
Non-polymers961
Water1086
1
A: DNA BINDING PROTEIN SSO10B
hetero molecules

A: DNA BINDING PROTEIN SSO10B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1744
Polymers21,9822
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_553x,-y+1/2,-z-7/41
MethodPQS
Unit cell
Length a, b, c (Å)84.680, 84.680, 87.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein DNA BINDING PROTEIN SSO10B / ALBA


Mass: 10990.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97ZF6, UniProt: P60849*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.9 Å3/Da / Density % sol: 68 %
Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Wardleworth, B.N., (2001) Acta Crystallogr.,Sect.D, 57, 1893.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
250 mMTris1droppH7.5
3300 mM1dropNaCl
418 %PEG80001reservoir
50.1 Msodium cacodylate1reservoirpH6.5
60.2 M1reservoirCaCl2
70.1 M1,2,3-heptanetriol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 4115 / % possible obs: 100 % / Redundancy: 23 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 23 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.4 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 100 % / Redundancy: 23.3 %
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.447

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H0X

1h0x


Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.295 417 10 %RANDOM
Rwork0.251 ---
obs0.251 4114 100 %-
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms690 0 5 6 701
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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