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- PDB-1rxw: Crystal structure of A. fulgidus FEN-1 bound to DNA -

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Basic information

Entry
Database: PDB / ID: 1rxw
TitleCrystal structure of A. fulgidus FEN-1 bound to DNA
Components
  • 5'-d(*C*pG*pA*pT*pG*pC*pT*pA)-3'
  • 5'-d(*T*pA*pG*pC*pA*pT*pC*pG*pG)-3'
  • Flap structure-specific endonuclease
KeywordsHYDROLASE/DNA / helical clamp / helix-3 turn-helix / hydrophobic wedge / 3' flap binding site / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / Hydrolases; Acting on ester bonds / DNA repair / magnesium ion binding / DNA binding
Similarity search - Function
Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap structure-specific endonuclease, archaea / Flap endonuclease 1 / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / 5'-nuclease / 5'-3' exonuclease / 5'-3' exonuclease / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / Flap endonuclease 1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChapados, B.R. / Hosfield, D.J. / Han, S. / Qiu, J. / Yelent, B. / Shen, B. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structural Basis for FEN-1 Substrate Specificity and PCNA-Mediated Activation in DNA Replication and Repair
Authors: Chapados, B.R. / Hosfield, D.J. / Han, S. / Qiu, J. / Yelent, B. / Shen, B. / Tainer, J.A.
History
DepositionDec 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 23, 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
B: 5'-d(*C*pG*pA*pT*pG*pC*pT*pA)-3'
C: 5'-d(*T*pA*pG*pC*pA*pT*pC*pG*pG)-3'
A: Flap structure-specific endonuclease


Theoretical massNumber of molelcules
Total (without water)43,3003
Polymers43,3003
Non-polymers00
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.330, 86.476, 43.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1117-

HOH

DetailsThe biological assembly is a monomer in the asymmetric unit.

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Components

#1: DNA chain 5'-d(*C*pG*pA*pT*pG*pC*pT*pA)-3'


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic upstream primer strand
#2: DNA chain 5'-d(*T*pA*pG*pC*pA*pT*pC*pG*pG)-3'


Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic upstream primer strand
#3: Protein Flap structure-specific endonuclease


Mass: 38117.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: FEN, AF0264 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29975
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, ammonium sulfate, glycerol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2ammonium sulfate11
3glycerol11
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
215 %PEG40001reservoir
3100 mMammonium sulfate1reservoir
415 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 24, 1999
RadiationMonochromator: Ge(111). conical Si/Rh mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 33233 / Num. obs: 33233 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.056
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.322 / % possible all: 97.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RXV

1rxv


Resolution: 2→40 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1313 -random
Rwork0.242 ---
obs0.245 26938 93.3 %-
all-28070 --
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 303 0 152 2889
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.09
X-RAY DIFFRACTIONx_torsion_deg19.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.83

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