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- PDB-5wvw: The crystal structure of Cren7 mutant L28A in complex with dsDNA -

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Basic information

Entry
Database: PDB / ID: 5wvw
TitleThe crystal structure of Cren7 mutant L28A in complex with dsDNA
Components
  • Chromatin protein Cren7
  • DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3')
KeywordsDNA BINDING PROTEIN/DNA / BETA-SHEET / DNA BINDING / 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 / Chromatin protein Cren7
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, Z.F. / Zhao, M.H. / Wang, L. / Chen, Y.Y. / Dong, Y.H. / Gong, Y. / Huang, L.
CitationJournal: Biochem. J. / Year: 2017
Title: Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA
Authors: Zhang, Z. / Zhao, M. / Wang, L. / Chen, Y. / Dong, Y. / Gong, Y. / Huang, L.
History
DepositionDec 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
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(*GP*TP*GP*AP*TP*CP*AP*C)-3')
D: DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3')
E: DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3')
F: DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)22,9786
Polymers22,9786
Non-polymers00
Water5,332296
1
A: Chromatin protein Cren7
C: DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3')
D: DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,4893
Polymers11,4893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-11 kcal/mol
Surface area5710 Å2
MethodPISA
2
B: Chromatin protein Cren7
E: DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3')
F: DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,4893
Polymers11,4893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-11 kcal/mol
Surface area5720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.511, 77.605, 104.173
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: 6635.834 Da / Num. of mol.: 2 / Mutation: L28A
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 / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 (DE3) / References: UniProt: Q97ZE3
#2: DNA chain
DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3')


Mass: 2426.617 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.: 296 / 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: 3.41 Å3/Da / Density % sol: 63.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 10% 2-Propanol, 0.1M BICINE pH8.5, 30% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 29759 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 48.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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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: 1.8→50 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.16
RfactorNum. reflection% reflection
Rfree0.2031 1493 5.07 %
Rwork0.184 --
obs0.185 29425 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 644 0 296 1848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081654
X-RAY DIFFRACTIONf_angle_d1.1622360
X-RAY DIFFRACTIONf_dihedral_angle_d23.843678
X-RAY DIFFRACTIONf_chiral_restr0.048252
X-RAY DIFFRACTIONf_plane_restr0.008192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85810.30981430.27922507X-RAY DIFFRACTION100
1.8581-1.92450.32751410.26932474X-RAY DIFFRACTION100
1.9245-2.00150.28081230.25012533X-RAY DIFFRACTION100
2.0015-2.09260.23031400.2232533X-RAY DIFFRACTION100
2.0926-2.20290.24831150.22662530X-RAY DIFFRACTION100
2.2029-2.34090.24061280.2172509X-RAY DIFFRACTION100
2.3409-2.52160.27561440.23622533X-RAY DIFFRACTION100
2.5216-2.77530.27121410.22462551X-RAY DIFFRACTION100
2.7753-3.17670.21381460.19992540X-RAY DIFFRACTION100
3.1767-4.00170.17271440.15422559X-RAY DIFFRACTION100
4.0017-37.77550.13951280.14012663X-RAY DIFFRACTION98

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