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- PDB-3u6y: Crystal structure of ALBA2-DNA complex -

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Basic information

Entry
Database: PDB / ID: 3u6y
TitleCrystal structure of ALBA2-DNA complex
Components
  • DNA (5'-D(*CP*CP*GP*GP*C)-3')
  • DNA (5'-D(*GP*GP*CP*CP*G)-3')
  • DNA/RNA-binding protein Alba 2
KeywordsDNA BINDING PROTEIN/DNA / ALBA 2 / Archaea / DNA-Binding Protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / DNA Binding Protein-DNA complex
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
PHOSPHATE ION / DNA / DNA/RNA-binding protein Alba 2
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKumarevel, T. / Tanaka, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of archaeal chromatin protein Alba2-double-stranded DNA complex from Aeropyrum pernix K1.
Authors: Tanaka, T. / Padavattan, S. / Kumarevel, T.
#1: Journal: Proteins / Year: 2008
Title: Crystal structure of an archaeal specific DNA-binding protein (Ape10b2) from Aeropyrum pernix K1.
Authors: Kumarevel, T. / Sakamoto, K. / Gopinath, S.C. / Shinkai, A. / Kumar, P.K. / Yokoyama, S.
History
DepositionOct 13, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Source and taxonomy / Category: citation / citation_author / pdbx_entity_src_syn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA/RNA-binding protein Alba 2
C: DNA/RNA-binding protein Alba 2
D: DNA (5'-D(*CP*CP*GP*GP*C)-3')
E: DNA (5'-D(*GP*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8915
Polymers25,7964
Non-polymers951
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.556, 74.290, 88.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA/RNA-binding protein Alba 2


Mass: 11397.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: albA2, APE_1823 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YAX2
#2: DNA chain DNA (5'-D(*CP*CP*GP*GP*C)-3')


Mass: 1481.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*GP*CP*CP*G)-3')


Mass: 1521.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M AMMONIUM DIHYDROGEN PHOSPHATE, PEG 3350, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2009 / Details: SI II CHANNEL
RadiationMonochromator: SI II CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 15617 / Num. obs: 15617 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 14.1 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 2→2.07 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.496 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H9U

2h9u


Resolution: 2→19.93 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1188968 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1106 7.1 %RANDOM
Rwork0.244 ---
obs0.244 15507 99.9 %-
all-15617 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.36 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 44.03 Å2
Baniso -1Baniso -2Baniso -3
1-7.05 Å20 Å20 Å2
2---2.12 Å20 Å2
3----4.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 199 5 183 1933
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it2.041.5
X-RAY DIFFRACTIONc_mcangle_it3.382
X-RAY DIFFRACTIONc_scbond_it2.642
X-RAY DIFFRACTIONc_scangle_it4.072.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.314 197 7.8 %
Rwork0.246 2332 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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