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- PDB-4r56: Crystal structure of Sulfolobus Cren7-dsDNA(GTGATCAC) complex -

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Basic information

Entry
Database: PDB / ID: 4r56
TitleCrystal structure of Sulfolobus Cren7-dsDNA(GTGATCAC) complex
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
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 (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, Z.F. / Gong, Y. / Chen, Y.Y. / Li, H.B. / Huang, L.
CitationJournal: Extremophiles / Year: 2015
Title: Insights into the interaction between Cren7 and DNA: the role of loop beta 3-beta 4
Authors: Zhang, Z.F. / Gong, Y. / Chen, Y.Y. / Li, H.B. / Huang, L.
History
DepositionAug 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2015Provider: 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*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)23,0626
Polymers23,0626
Non-polymers00
Water2,090116
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)11,5313
Polymers11,5313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-11 kcal/mol
Surface area5690 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)11,5313
Polymers11,5313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-12 kcal/mol
Surface area5690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.913, 77.922, 104.429
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) / Gene: creN7, SSO6901 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) plysS / 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 (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 30% PEG 1500, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 16, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 14498 / Num. obs: 14194 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 37.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1354 / % possible all: 96.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWH

3lwh


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.237 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.232 716 5.1 %RANDOM
Rwork0.2 ---
all0.202 13798 --
obs0.202 13431 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.169 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20 Å2
2---0 Å2-0 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 644 0 116 1686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0161672
X-RAY DIFFRACTIONr_bond_other_d0.0010.021344
X-RAY DIFFRACTIONr_angle_refined_deg1.321.6262384
X-RAY DIFFRACTIONr_angle_other_deg4.95733156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2185116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.03823.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68415184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.844154
X-RAY DIFFRACTIONr_chiral_restr0.070.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211378
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02326
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_it2.5964.446470
X-RAY DIFFRACTIONr_mcbond_other2.5954.445469
X-RAY DIFFRACTIONr_mcangle_it4.0546.661584
X-RAY DIFFRACTIONr_mcangle_other4.0526.661585
X-RAY DIFFRACTIONr_scbond_it2.6023.9511202
X-RAY DIFFRACTIONr_scbond_other2.6033.9511201
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9255.8161800
X-RAY DIFFRACTIONr_long_range_B_refined5.86434.3862051
X-RAY DIFFRACTIONr_long_range_B_other5.82534.252012
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.296→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 59 -
Rwork0.345 902 -
obs--91.87 %

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