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- PDB-4r55: The crystal structure of a Cren7 mutant protein GR and dsDNA complex -

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Basic information

Entry
Database: PDB / ID: 4r55
TitleThe crystal structure of a Cren7 mutant protein GR and dsDNA 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: 1.8 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromatin protein Cren7
B: DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3')
C: DNA (5'-D(*GP*TP*GP*AP*TP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,0483
Polymers11,0483
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.495, 41.790, 54.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chromatin protein Cren7


Mass: 6194.311 Da / Num. of mol.: 1 / Mutation: DELETION
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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M NH4Ac, 0.01M MgAc2, 0.05M sodium cacodylate trihydrate, 30% PEG 8000, pH 6.5, 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: May 17, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 9449 / Num. obs: 9402 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 40.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 25.3 / Num. unique all: 918 / % possible all: 99

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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: 1.8→17 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.893 / SU B: 2.857 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.152 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.252 448 4.8 %RANDOM
Rwork0.219 ---
all0.22 8964 --
obs0.22 8922 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.603 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms423 322 0 72 817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.015795
X-RAY DIFFRACTIONr_bond_other_d0.0010.02627
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.6041138
X-RAY DIFFRACTIONr_angle_other_deg1.09131470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.525552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.63423.33315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.6771583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.278152
X-RAY DIFFRACTIONr_chiral_restr0.1040.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021646
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02158
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_it1.2411.144211
X-RAY DIFFRACTIONr_mcbond_other1.2421.141210
X-RAY DIFFRACTIONr_mcangle_it1.8951.704262
X-RAY DIFFRACTIONr_mcangle_other1.8931.706263
X-RAY DIFFRACTIONr_scbond_it1.5311.237584
X-RAY DIFFRACTIONr_scbond_other1.5321.237583
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3341.807876
X-RAY DIFFRACTIONr_long_range_B_refined3.43810.341993
X-RAY DIFFRACTIONr_long_range_B_other3.42310.228964
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 34 -
Rwork0.201 633 -
obs--98.23 %

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