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- PDB-1b43: FEN-1 FROM P. FURIOSUS -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1b43
TitleFEN-1 FROM P. FURIOSUS
ComponentsPROTEIN (FEN-1)
KeywordsTRANSFERASE / NUCLEASE / DNA REPAIR / DNA REPLICATION
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 / 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
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsHosfield, D.J. / Mol, C.D. / Shen, B. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity.
Authors: Hosfield, D.J. / Mol, C.D. / Shen, B. / Tainer, J.A.
History
DepositionJan 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: PROTEIN (FEN-1)
B: PROTEIN (FEN-1)


Theoretical massNumber of molelcules
Total (without water)77,5982
Polymers77,5982
Non-polymers00
Water7,440413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.820, 122.040, 134.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.1574, -0.9873, -0.0205), (-0.9875, -0.1574, -0.0015), (-0.0018, 0.0205, -0.9998)
Vector: 103.24, 120.437, 32.715)

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Components

#1: Protein PROTEIN (FEN-1)


Mass: 38798.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RESIDUE 1 IN THE STRUCTURE IS THE FIRST ORDERED RESIDUE, WHICH CORRESPONDS TO GLY2 IN THE SEQUENCE.
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PET15-B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O93634
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 6.5
Details: 60 % AMMONIUM SULFATE 100 MM IMIDAZOLE MALATE 50 MM MGCL2, pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mg/mlprotease1drop
260 %satammonium sulfate1reservoirprecipitant
350 mM1reservoirprecipitantMgCl2
4100 mMimidazole/malate1reservoirprecipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 62063 / % possible obs: 96 % / Redundancy: 3.4 % / Biso Wilson estimate: 62.3 Å2 / Rsym value: 0.038 / Net I/σ(I): 15
Reflection shellResolution: 2→2.07 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.346 / % possible all: 88.3
Reflection
*PLUS
Num. measured all: 208396 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 88.3 % / Rmerge(I) obs: 0.346

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 -10 %RANDOM
Rwork0.231 ---
obs0.231 61482 96 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5444 0 0 413 5857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.42
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3272 749 10 %
Rwork0.3266 6378 -
obs--95.5 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PAR

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