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- PDB-5wwc: The crystal structure of Cren7 mutant L28M in complex with dsDNA -

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Basic information

Entry
Database: PDB / ID: 5wwc
TitleThe crystal structure of Cren7 mutant L28M in complex with dsDNA
Components
  • Chromatin protein Cren7
  • DNA (5'-D(*GP*TP*AP*AP*TP*TP*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


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: 1.9 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 31, 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*AP*AP*TP*TP*AP*C)-3')
D: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
E: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
F: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)23,0946
Polymers23,0946
Non-polymers00
Water1,53185
1
A: Chromatin protein Cren7
C: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
D: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,5473
Polymers11,5473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-14 kcal/mol
Surface area5810 Å2
MethodPISA
2
B: Chromatin protein Cren7
E: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
F: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,5473
Polymers11,5473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-13 kcal/mol
Surface area5730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.167, 52.370, 57.016
Angle α, β, γ (deg.)90.00, 94.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Chromatin protein Cren7 /


Mass: 6695.952 Da / Num. of mol.: 2 / Mutation: L28M
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*AP*AP*TP*TP*AP*C)-3')


Mass: 2425.629 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 30% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 14394 / % possible obs: 99.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 3.9 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWH

3lwh


Resolution: 1.9→50 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.45
RfactorNum. reflection% reflection
Rfree0.2347 722 5.03 %
Rwork0.1975 --
obs0.1995 14362 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 644 0 85 1631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011648
X-RAY DIFFRACTIONf_angle_d1.222353
X-RAY DIFFRACTIONf_dihedral_angle_d27.798675
X-RAY DIFFRACTIONf_chiral_restr0.055252
X-RAY DIFFRACTIONf_plane_restr0.008191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.04660.3271440.26282659X-RAY DIFFRACTION97
2.0466-2.25250.3231390.24492735X-RAY DIFFRACTION99
2.2525-2.57820.27191360.2362723X-RAY DIFFRACTION99
2.5782-3.24730.26111460.22852752X-RAY DIFFRACTION100
3.2473-26.31050.19491570.16342771X-RAY DIFFRACTION99

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