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- PDB-2bky: Crystal structure of the Alba1:Alba2 heterodimer from sulfolobus ... -

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Basic information

Entry
Database: PDB / ID: 2bky
TitleCrystal structure of the Alba1:Alba2 heterodimer from sulfolobus solfataricus
Components
  • DNA/RNA-BINDING PROTEIN ALBA 1
  • DNA/RNA-BINDING PROTEIN ALBA 2
KeywordsDNA BINDING PROTEIN / ARCHAEAL DNA BINDING PROTEIN / DNA CONDENSATION / DNA-BINDING / RNA-BINDING
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 2
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJelinska, C. / Conroy, M.J. / Craven, C.J. / Bullough, P.A. / Waltho, J.P. / Taylor, G.L. / White, M.F.
CitationJournal: Structure / Year: 2005
Title: Obligate Heterodimerization of the Archaeal Alba2 Protein with Alba1 Provides a Mechanism for Control of DNA Packaging.
Authors: Jelinska, C. / Conroy, M.J. / Craven, C.J. / Hounslow, A.M. / Bullough, P.A. / Waltho, J.P. / Taylor, G.L. / White, M.F.
History
DepositionFeb 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2005Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: DNA/RNA-BINDING PROTEIN ALBA 1
B: DNA/RNA-BINDING PROTEIN ALBA 1
X: DNA/RNA-BINDING PROTEIN ALBA 2
Y: DNA/RNA-BINDING PROTEIN ALBA 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3069
Polymers41,7154
Non-polymers5915
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-68.9 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.788, 102.788, 66.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DNA/RNA-BINDING PROTEIN ALBA 1 / ALBA HETERODIMER / SSO10B


Mass: 10601.442 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PET 30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: P60849
#2: Protein DNA/RNA-BINDING PROTEIN ALBA 2 / ALBA HETERODIMER


Mass: 10255.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PET 30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q97ZF4
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: BINDS DNA DOUBLE-STRAND TIGHTLY BUT WITHOUT SEQUENCE SPECIFICITY

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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: 2.19 Å3/Da / Density % sol: 43.36 %
Crystal growpH: 7.5 / Details: 35% MPD, 50MM HEPES, 10MM TRIS, 100MM NACL, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.7→36.8 Å / Num. obs: 44420 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 10.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→87.71 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2208 5 %RANDOM
Rwork0.17 ---
obs0.172 42333 99.2 %-
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: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.7→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 40 324 3136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223015
X-RAY DIFFRACTIONr_bond_other_d0.0030.023030
X-RAY DIFFRACTIONr_angle_refined_deg1.8751.994073
X-RAY DIFFRACTIONr_angle_other_deg0.99237008
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9285383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1380.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023306
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02592
X-RAY DIFFRACTIONr_nbd_refined0.2360.2556
X-RAY DIFFRACTIONr_nbd_other0.2510.23758
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.22145
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2650.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.9520.287
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5750.2247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5430.264
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.171.51851
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.11423043
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.09331164
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1594.51029
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.253 154
Rwork0.199 3099

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