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- PDB-5wvy: The crystal structure of Cren7 mutant L28V in complex with dsDNA -

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Basic information

Entry
Database: PDB / ID: 5wvy
TitleThe crystal structure of Cren7 mutant L28V 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 / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 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

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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)23,0346
Polymers23,0346
Non-polymers00
Water3,783210
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)11,5173
Polymers11,5173
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-12 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)11,5173
Polymers11,5173
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-13 kcal/mol
Surface area5710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.884, 78.867, 104.218
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: 6663.887 Da / Num. of mol.: 2 / Mutation: L28V
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 (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.: 210 / 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: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1M Sodium acetate pH4.6, 40% PEG200

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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: Apr 11, 2013
RadiationProtocol: 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: 22094 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 37.3
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2 / % possible all: 91

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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→50 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / Phase error: 27.59
RfactorNum. reflection% reflection
Rfree0.236 1122 5.08 %
Rwork0.1749 --
obs0.1777 22094 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 644 0 210 1778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091670
X-RAY DIFFRACTIONf_angle_d1.142382
X-RAY DIFFRACTIONf_dihedral_angle_d23.763684
X-RAY DIFFRACTIONf_chiral_restr0.051256
X-RAY DIFFRACTIONf_plane_restr0.007194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0910.35211240.28412432X-RAY DIFFRACTION94
2.091-2.20110.28881320.24212621X-RAY DIFFRACTION100
2.2011-2.33890.26731530.22932599X-RAY DIFFRACTION100
2.3389-2.51930.31631550.22462601X-RAY DIFFRACTION100
2.5193-2.77240.26911510.22162613X-RAY DIFFRACTION100
2.7724-3.17260.27361430.20422634X-RAY DIFFRACTION100
3.1726-3.99350.23331350.1662697X-RAY DIFFRACTION100
3.9935-22.50110.16721290.12572775X-RAY DIFFRACTION100

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