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- PDB-1mc8: Crystal Structure of Flap Endonuclease-1 R42E mutant from Pyrococ... -

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Basic information

Entry
Database: PDB / ID: 1mc8
TitleCrystal Structure of Flap Endonuclease-1 R42E mutant from Pyrococcus horikoshii
ComponentsFlap Endonuclease-1
KeywordsHYDROLASE / flexible loop
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 horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMatsui, E. / Musti, K.V. / Abe, J. / Yamazaki, K. / Matsui, I. / Harata, K.
CitationJournal: J.BIOL.CHEM. / Year: 2002
Title: Molecular Structure and Novel DNA Binding Sites Located in Loops of Flap Endonuclease-1 from Pyrococcus horikoshii
Authors: Matsui, E. / Musti, K.V. / Abe, J. / Yamazaki, K. / Matsui, I. / Harata, K.
History
DepositionAug 6, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Flap Endonuclease-1
B: Flap Endonuclease-1


Theoretical massNumber of molelcules
Total (without water)77,9602
Polymers77,9602
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)62.67, 62.67, 180.69
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Flap Endonuclease-1 / 5' nuclease


Mass: 38980.082 Da / Num. of mol.: 2 / Mutation: R42E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: O50123

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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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG6000, sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 %protein1drop
2200 mM1droppH8.0NaCl
350 mMTris-HCl1droppH6.0
420 %PEG60001reservoirpH6.0
5100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→34.7 Å / Num. all: 15903 / Num. obs: 15903 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.104
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.494 / % possible all: 98.6
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 135478 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
Rmerge(I) obs: 0.494

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
X-PLORmodel building
X-PLORrefinement
CCP4(TRUNCATE)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A76

1a76


Resolution: 3.1→8 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 1339 random
Rwork0.19 --
obs0.197 13576 -
all-14415 -
Displacement parametersBiso mean: 37.8 Å2
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5274 0 0 0 5274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_improper_angle_d1.93
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
LS refinement shellResolution: 3.1→3.15 Å
RfactorNum. reflection% reflection
Rfree0.458 76 -
Rwork0.328 --
obs-596 88.7 %
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 8 Å / Rfactor obs: 0.197 / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.93
LS refinement shell
*PLUS
Rfactor Rfree: 0.458 / Rfactor Rwork: 0.328

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