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- PDB-5k07: Crystal structure of CREN7-DSDNA (GTAATTGC) complex -

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Basic information

Entry
Database: PDB / ID: 5k07
TitleCrystal structure of CREN7-DSDNA (GTAATTGC) complex
Components
  • Chromatin protein Cren7
  • DNA (5'-D(*GP*TP*AP*AP*TP*TP*GP*C)-3')
KeywordsDNA BINDING PROTEIN/DNA / PROTEIN-DNA COMPLEX / BETA-SHEET / DNA-BINDING / METHYLATION / DNA BINDING PROTEIN-DNA COMPLEX
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 / Chromatin protein Cren7
Similarity search - Component
Biological speciesSulfolobus solfataricus P2 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, Z.F. / Gong, Y.
CitationJournal: PLoS ONE / Year: 2016
Title: Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea
Authors: Tian, L. / Zhang, Z.F. / Wang, H. / Zhao, M. / Dong, Y. / Gong, Y.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: DNA (5'-D(*GP*TP*AP*AP*TP*TP*GP*C)-3')
C: DNA (5'-D(*GP*TP*AP*AP*TP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,5613
Polymers11,5613
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-11 kcal/mol
Surface area5940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.795, 52.867, 90.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Chromatin protein Cren7


Mass: 6677.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus P2 (archaea) / Strain: P2 / Gene: creN7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZE3
#2: DNA chain DNA (5'-D(*GP*TP*AP*AP*TP*TP*GP*C)-3')


Mass: 2441.628 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.: 97 / 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: 2.68 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 30% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 7, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 8403 / % possible obs: 96 % / Redundancy: 6.5 % / Net I/σ(I): 16.4
Reflection shellResolution: 2→2.07 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWH

3lwh


Resolution: 2→15 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.35
RfactorNum. reflection% reflection
Rfree0.2298 392 5 %
Rwork0.1977 --
obs0.1991 8354 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms451 324 0 98 873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008826
X-RAY DIFFRACTIONf_angle_d1.0611180
X-RAY DIFFRACTIONf_dihedral_angle_d24.094339
X-RAY DIFFRACTIONf_chiral_restr0.046126
X-RAY DIFFRACTIONf_plane_restr0.00695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0022-2.29110.25921170.21572585X-RAY DIFFRACTION95
2.2911-2.88310.24821420.26242644X-RAY DIFFRACTION97
2.8831-14.9560.21741330.17482733X-RAY DIFFRACTION97

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