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- PDB-1rxz: C-terminal region of A. fulgidus FEN-1 complexed with A. fulgidus PCNA -

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Basic information

Entry
Database: PDB / ID: 1rxz
TitleC-terminal region of A. fulgidus FEN-1 complexed with A. fulgidus PCNA
Components
  • DNA polymerase sliding clamp
  • Flap structure-specific endonuclease
KeywordsREPLICATION / beta-zipper / interdomain connecting loop / DNA repair / DNA replication
Function / homology
Function and homology information


5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / 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 / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / PIN-like domain superfamily / : / Alpha Beta
Similarity search - Domain/homology
DNA polymerase sliding clamp / 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 1.3Aug 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

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Assembly

Deposited unit
A: DNA polymerase sliding clamp
B: Flap structure-specific endonuclease


Theoretical massNumber of molelcules
Total (without water)28,6702
Polymers28,6702
Non-polymers00
Water1,60389
1
A: DNA polymerase sliding clamp
B: Flap structure-specific endonuclease

A: DNA polymerase sliding clamp
B: Flap structure-specific endonuclease

A: DNA polymerase sliding clamp
B: Flap structure-specific endonuclease


Theoretical massNumber of molelcules
Total (without water)86,0106
Polymers86,0106
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Unit cell
Length a, b, c (Å)86.530, 86.530, 96.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by applying the following transformations: ROTATION: [-0.5 -0.86603 0] [0.86603 -0.5 0] [0 0 1] TRANSLATION: 86.53304 -0.00002 0.00002 AND ROTATION: [-0.5 0.86603 0] [-0.86603 -0.5 0] [0 0 1] TRANSLATION: 43.26651 74.9398 0.00003

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Components

#1: Protein DNA polymerase sliding clamp / Proliferating cell nuclear antigen homolog / PCNA


Mass: 27301.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: PCN, AF0335 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29912
#2: Protein/peptide Flap structure-specific endonuclease


Mass: 1368.536 Da / Num. of mol.: 1 / Fragment: PCNA-binding motif / Source method: obtained synthetically
Details: synthetic peptide derived from the PCNA-binding motif of afFEN-1
References: UniProt: O29975
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Na/K phosphate, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
250 mMTris1droppH8.0
3250 mM1dropNaCl
41.4-1.6 Msodium/pootassium phosphate1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2003
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. all: 36466 / Num. obs: 36466 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.08
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.457 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RWZ

1rwz


Resolution: 2→60 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Carried out twinned refinement in CNS, against the least squares residual for hemihedral twinning. The twinning operator is: h,-h-k,-l. The twin fraction is: 0.370
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3472 -randomly selected in the shells to ensure that twin-related reflections were selected in pairs
Rwork0.18 ---
all0.189 36330 --
obs0.189 36330 99.4 %-
Refinement stepCycle: LAST / Resolution: 2→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 0 89 2102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.29
X-RAY DIFFRACTIONx_torsion_deg25.3
X-RAY DIFFRACTIONx_torsion_impr_deg0.74
Refinement
*PLUS
Rfactor Rfree: 0.26 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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