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- PDB-2qnf: Crystal structure of T4 Endonuclease VII H43N mutant in complex w... -

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Basic information

Entry
Database: PDB / ID: 2qnf
TitleCrystal structure of T4 Endonuclease VII H43N mutant in complex with heteroduplex DNA containing base mismatches
Components
  • DNA (5'-D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DG)-3')
  • DNA (5'-D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DGP*DC)-3')
  • DNA (5'-D(*DCP*DGP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DTP*DG)-3')
  • DNA (5'-D(*DGP*DCP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DTP*DG)-3')
  • Recombination endonuclease VII
KeywordsHydrolase/DNA / T4 Endonuclease VII / Endo VII / resolvase / resolving-enzyme / DNA mismatch / Alternative initiation / Calcium / Hydrolase / Metal-binding / Zinc / Hydrolase-DNA COMPLEX
Function / homology
Function and homology information


endonuclease activity / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
T4 recombination endonuclease VII, dimerisation / T4 recombination endonuclease VII, dimerisation domain superfamily / T4 recombination endonuclease VII, dimerisation / His-Me finger endonucleases / Recombination endonuclease VII / Recombination endonuclease VII superfamily / Recombination endonuclease VII / His-Me finger endonuclease fold / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 ...T4 recombination endonuclease VII, dimerisation / T4 recombination endonuclease VII, dimerisation domain superfamily / T4 recombination endonuclease VII, dimerisation / His-Me finger endonucleases / Recombination endonuclease VII / Recombination endonuclease VII superfamily / Recombination endonuclease VII / His-Me finger endonuclease fold / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #10 / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / His-Me finger superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Recombination endonuclease VII
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBiertumpfel, C. / Yang, W. / Suck, D.
CitationJournal: Nature / Year: 2007
Title: Crystal structure of T4 endonuclease VII resolving a Holliday junction.
Authors: Biertumpfel, C. / Yang, W. / Suck, D.
History
DepositionJul 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DG)-3')
D: DNA (5'-D(*DGP*DCP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DTP*DG)-3')
E: DNA (5'-D(*DCP*DGP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DTP*DG)-3')
F: DNA (5'-D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DGP*DC)-3')
A: Recombination endonuclease VII
B: Recombination endonuclease VII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0278
Polymers55,8966
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.997, 64.997, 153.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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DNA chain , 4 types, 4 molecules CDEF

#1: DNA chain DNA (5'-D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DCP*DG)-3')


Mass: 4908.193 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DGP*DCP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DTP*DG)-3')


Mass: 4890.166 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*DCP*DGP*DGP*DCP*DTP*DCP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DTP*DG)-3')


Mass: 4890.166 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain DNA (5'-D(*DCP*DAP*DCP*DAP*DTP*DCP*DGP*DAP*DTP*DGP*DGP*DAP*DGP*DCP*DGP*DC)-3')


Mass: 4908.193 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein / Non-polymers , 2 types, 4 molecules AB

#5: Protein Recombination endonuclease VII / Endo VII / Protein Gp49


Mass: 18149.732 Da / Num. of mol.: 2 / Mutation: H43N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 49 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P13340, crossover junction endodeoxyribonuclease
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.35 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 25%(w/v) PEG 3350, 100 mM Bis-Tris, 220mM Li2SO4 and 5% (w/v) glucose, pH 6.5, VAPOR DIFFUSION, temperature 293K, pH 6.50
Components of the solutions
IDNameCrystal-IDSol-ID
1Li2SO411
2PEG 335011
3Bis-Tris11
4glucose11
5glucose12
6PEG 335012
7Bis-Tris12
8glucose12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2006
RadiationMonochromator: SI 220. ROSENBAUM-ROCK DOUBLE -CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→38 Å / Num. obs: 12214 / % possible obs: 84.6 % / Redundancy: 2.89 % / Biso Wilson estimate: 88.4 Å2 / Rsym value: 0.048 / Net I/σ(I): 20.8
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 5.7 / Rsym value: 0.146 / % possible all: 37.6

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Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E7L

1e7l


Resolution: 3→37.84 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1930098.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1257 10.3 %RANDOM
Rwork0.246 ---
obs0.246 12214 84.1 %-
all-12195 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.02 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 134.2 Å2
Baniso -1Baniso -2Baniso -3
1-38.37 Å20 Å20 Å2
2--38.37 Å20 Å2
3----76.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.68 Å0.52 Å
Luzzati d res low-40 Å
Luzzati sigma a0.8 Å0.74 Å
Refinement stepCycle: LAST / Resolution: 3→37.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 1300 2 0 3842
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.321.5
X-RAY DIFFRACTIONc_mcangle_it3.842
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.62.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.558 99 9.8 %
Rwork0.52 914 -
obs--41.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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