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- PDB-5k17: Crystal structure of CREN7-DSDNA (GTGATCGC) complex -

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Basic information

Entry
Database: PDB / ID: 5k17
TitleCrystal structure of CREN7-DSDNA (GTGATCGC) complex
Components
  • Chromatin protein Cren7
  • DNA (5'-D(*GP*TP*GP*AP*TP*CP*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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Chromatin protein Cren7
C: DNA (5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3')
D: DNA (5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3')
E: DNA (5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3')
F: DNA (5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)23,1266
Polymers23,1266
Non-polymers00
Water2,252125
1
A: Chromatin protein Cren7
C: DNA (5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3')
D: DNA (5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,5633
Polymers11,5633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-12 kcal/mol
Surface area5720 Å2
MethodPISA
2
B: Chromatin protein Cren7
E: DNA (5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3')
F: DNA (5'-D(*GP*TP*GP*AP*TP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,5633
Polymers11,5633
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-12 kcal/mol
Surface area5730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.694, 77.676, 104.268
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.: 2
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*GP*AP*TP*CP*GP*C)-3')


Mass: 2442.616 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 18763 / % possible obs: 99.9 % / Redundancy: 8.1 % / Net I/σ(I): 3.82
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWH

3lwh


Resolution: 2.1→38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.132 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 944 5 %RANDOM
Rwork0.196 ---
obs0.19636 17794 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.666 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2--2.06 Å20 Å2
3----4.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 648 0 126 1700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0161676
X-RAY DIFFRACTIONr_bond_other_d0.0010.021344
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.6212392
X-RAY DIFFRACTIONr_angle_other_deg3.94133156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6815116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.65523.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92115184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.651154
X-RAY DIFFRACTIONr_chiral_restr0.0490.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211382
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02326
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0784.764470
X-RAY DIFFRACTIONr_mcbond_other3.0654.76469
X-RAY DIFFRACTIONr_mcangle_it4.357.116584
X-RAY DIFFRACTIONr_mcangle_other4.3537.118585
X-RAY DIFFRACTIONr_scbond_it3.1644.2591206
X-RAY DIFFRACTIONr_scbond_other3.1654.261205
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2296.2891808
X-RAY DIFFRACTIONr_long_range_B_refined5.70437.542097
X-RAY DIFFRACTIONr_long_range_B_other5.65137.3832052
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 66 -
Rwork0.284 1267 -
obs--98.45 %

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