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- PDB-2p6u: Apo structure of the Hel308 superfamily 2 helicase -

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Basic information

Entry
Database: PDB / ID: 2p6u
TitleApo structure of the Hel308 superfamily 2 helicase
ComponentsafuHEL308 HELICASE
KeywordsDNA BINDING PROTEIN / archaeal Helicase / SF2 helicase / DNA repair
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 / MAD / Resolution: 3.14 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
A: afuHEL308 HELICASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,07311
Polymers79,1231
Non-polymers95010
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.150, 136.150, 230.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: 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)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.97 Å3/Da / Density % sol: 68.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M NaCitrate pH 5.6; 1 M (NH4)2PO4; 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONESRF ID2920.9797, 0.9795
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDFeb 12, 2006
ADSC QUANTUM 2102CCDFeb 12, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97971
30.97951
ReflectionResolution: 3.14→20 Å / Num. obs: 22283 / % possible obs: 46.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.086 / Rsym value: 0.081
Reflection shellHighest resolution: 3.14 Å / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 62.2 / Rsym value: 0.196 / % possible all: 94

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.14→20 Å / σ(F): 390 / σ(I): 2
RfactorNum. reflection% reflection
Rfree0.276 1062 4.5 %
Rwork0.23 --
all-22283 -
obs-21877 93 %
Solvent computationBsol: 22.206 Å2
Displacement parametersBiso mean: 57.613 Å2
Baniso -1Baniso -2Baniso -3
1-7.898 Å2-10.942 Å20 Å2
2--7.898 Å20 Å2
3----15.796 Å2
Refinement stepCycle: LAST / Resolution: 3.14→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5318 0 50 0 5368
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.656
X-RAY DIFFRACTIONc_mcbond_it1.4691.5
X-RAY DIFFRACTIONc_scbond_it1.8052
X-RAY DIFFRACTIONc_mcangle_it2.6222
X-RAY DIFFRACTIONc_scangle_it3.0682.5
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

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