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- PDB-2p6r: Crystal structure of superfamily 2 helicase Hel308 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2p6r
TitleCrystal structure of superfamily 2 helicase Hel308 in complex with unwound DNA
Components
  • 25-MER
  • 5'-D(*CP*TP*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3'
  • afUHEL308 HELICASE
KeywordsDNA binding protein/DNA / PROTEIN-DNA COMPLEX / SF2 HELICASE / ARCHAEAL HELICASE / DNA REPAIR / DNA binding protein-DNA COMPLEX
Function / homology
Function and homology information


Sec63 N-terminal domain-like fold - #30 / Sec63 N-terminal domain-like fold / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBuettner, K. / Nehring, S. / Hopfner, K.P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural basis for DNA duplex separation by a superfamily-2 helicase.
Authors: Buttner, K. / Nehring, S. / Hopfner, K.P.
History
DepositionMar 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE RESIDUES 1-691 MATCH THE GENBANK ACCESSION NP_071282. NO SUITABLE UNIPROT SEQUENCE ...SEQUENCE RESIDUES 1-691 MATCH THE GENBANK ACCESSION NP_071282. NO SUITABLE UNIPROT SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS ENTRY

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: 25-MER
Y: 5'-D(*CP*TP*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3'
A: afUHEL308 HELICASE


Theoretical massNumber of molelcules
Total (without water)91,3743
Polymers91,3743
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.379, 138.379, 252.973
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain 25-MER


Mass: 7657.960 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*AP*GP*AP*GP*AP*CP*TP*AP*TP*CP*GP*AP*T)-3'


Mass: 4593.011 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein afUHEL308 HELICASE


Mass: 79122.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pET-29 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)

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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: 3.86 Å3/Da / Density % sol: 68.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES pH 6.0; 22% MPD; 0.1M MgAcetate; 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2MPD11
3MgAcetate11
4Glycerol11
5H2O11
6MES12
7MPD12
8MgAcetate12
9Glycerol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 54172 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.089 / Rsym value: 0.09 / Net I/σ(I): 16.93
Reflection shellHighest resolution: 3 Å / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 8.97 / Rsym value: 0.194 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / σ(F): 611 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2748 2883 9.8 %
Rwork0.2317 --
obs-54172 97.9 %
Solvent computationBsol: 25.606 Å2
Displacement parametersBiso mean: 59.128 Å2
Baniso -1Baniso -2Baniso -3
1--3.49 Å2-12.242 Å20 Å2
2---3.49 Å20 Å2
3---6.98 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5406 813 0 0 6219
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.258
X-RAY DIFFRACTIONc_mcbond_it1.4251.5
X-RAY DIFFRACTIONc_scbond_it1.9482
X-RAY DIFFRACTIONc_mcangle_it2.4632
X-RAY DIFFRACTIONc_scangle_it3.092.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION3CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top

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