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- PDB-6a2i: Architectural roles of Cren7 in folding crenarchaeal chromatin fi... -

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Basic information

Entry
Database: PDB / ID: 6a2i
TitleArchitectural roles of Cren7 in folding crenarchaeal chromatin filament
Components
  • Chromatin protein Cren7
  • DNA (5'-D(*CP*GP*TP*AP*GP*CP*TP*AP*AP*TP*TP*AP*GP*CP*TP*AP*CP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / BETA-SHEET / DNA BINDING PROTEIN-DNA COMPLEX / Crenarchaeal chromatin protein
Function / homology
Function and homology information


chromosome / double-stranded DNA binding / cytoplasm
Similarity search - Function
Chromatin protein Cren7 / Double-stranded DNA-binding Cren7 / Cren7 superfamily / Chromatin protein Cren7 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Chromatin protein Cren7
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZhang, Z.F. / Zhao, M.H. / Chen, Y.Y. / Wang, L. / Dong, Y.H. / Gong, Y. / Huang, L.
CitationJournal: Mol. Microbiol. / Year: 2019
Title: Architectural roles of Cren7 in folding crenarchaeal chromatin filament.
Authors: Zhang, Z. / Zhao, M. / Chen, Y. / Wang, L. / Liu, Q. / Dong, Y. / Gong, Y. / Huang, L.
History
DepositionJun 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Chromatin protein Cren7
B: Chromatin protein Cren7
C: DNA (5'-D(*CP*GP*TP*AP*GP*CP*TP*AP*AP*TP*TP*AP*GP*CP*TP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*AP*GP*CP*TP*AP*AP*TP*TP*AP*GP*CP*TP*AP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)24,3874
Polymers24,3874
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-17 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.963, 29.940, 79.287
Angle α, β, γ (deg.)90.00, 123.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chromatin protein Cren7


Mass: 6677.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: creN7, SSO6901 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q97ZE3
#2: DNA chain DNA (5'-D(*CP*GP*TP*AP*GP*CP*TP*AP*AP*TP*TP*AP*GP*CP*TP*AP*CP*G)-3')


Mass: 5515.591 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.05M KH2PO4, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 9361 / % possible obs: 99.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 54.8
Reflection shellResolution: 2.4→2.45 Å / Rmerge(I) obs: 0.484

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWH

3lwh


Resolution: 2.4→50 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.38
RfactorNum. reflection% reflection
Rfree0.2607 431 4.78 %
Rwork0.2246 --
obs0.2263 9025 99.22 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 39.742 Å2 / ksol: 0.299 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.2894 Å20 Å21.3716 Å2
2--40.2657 Å20 Å2
3----21.9763 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms898 732 0 2 1632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031744
X-RAY DIFFRACTIONf_angle_d0.7972505
X-RAY DIFFRACTIONf_dihedral_angle_d25.011725
X-RAY DIFFRACTIONf_chiral_restr0.04270
X-RAY DIFFRACTIONf_plane_restr0.004193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.74710.44611520.39942824X-RAY DIFFRACTION100
2.7471-3.460.3271270.24412867X-RAY DIFFRACTION100
3.46-27.96720.22091520.19482903X-RAY DIFFRACTION98

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