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- PDB-3ory: Crystal structure of Flap endonuclease 1 from hyperthermophilic a... -

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Basic information

Entry
Database: PDB / ID: 3ory
TitleCrystal structure of Flap endonuclease 1 from hyperthermophilic archaeon Desulfurococcus amylolyticus
Componentsflap endonuclease 1
KeywordsHYDROLASE / endonuclease
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
PHOSPHATE ION / Flap endonuclease 1
Similarity search - Component
Biological speciesDesulfurococcus amylolyticus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMase, T. / Kubota, K. / Miyazono, K. / Kawarabayashii, Y. / Tanokura, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of flap endonuclease 1 from the hyperthermophilic archaeon Desulfurococcus amylolyticus
Authors: Mase, T. / Kubota, K. / Miyazono, K. / Kawarabayasi, Y. / Tanokura, M.
History
DepositionSep 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Mar 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1644
Polymers40,8791
Non-polymers2853
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: flap endonuclease 1
hetero molecules

A: flap endonuclease 1
hetero molecules

A: flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,49212
Polymers122,6373
Non-polymers8559
Water543
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
Buried area4090 Å2
ΔGint-22 kcal/mol
Surface area46320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.760, 103.760, 84.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein flap endonuclease 1


Mass: 40879.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfurococcus amylolyticus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: F2Z289*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN FROM DESULFUROCOCCUS AMYLOLYTICUS DOES NOT CURRENTLY EXIST.

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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: 3.22 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.1M Tris-HCl, 1.98M ammonium dihydrogen phosphate, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2008
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 35852 / % possible obs: 99.8 % / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.06 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.098 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22464 1793 5 %RANDOM
Rwork0.21034 ---
obs0.21106 34057 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.029 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2701 0 15 101 2817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222762
X-RAY DIFFRACTIONr_angle_refined_deg1.11923735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8675341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04624.417120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61415513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0911519
X-RAY DIFFRACTIONr_chiral_restr0.0760.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212043
X-RAY DIFFRACTIONr_mcbond_it0.5921.51704
X-RAY DIFFRACTIONr_mcangle_it1.13822756
X-RAY DIFFRACTIONr_scbond_it1.75731058
X-RAY DIFFRACTIONr_scangle_it3.0674.5979
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 134 -
Rwork0.264 2445 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 23.622 Å / Origin y: 40.091 Å / Origin z: 18.71 Å
111213212223313233
T0.0511 Å20.0408 Å20.011 Å2-0.1011 Å2-0.013 Å2--0.0387 Å2
L0.8261 °2-0.4812 °20.0302 °2-0.7657 °2-0.1133 °2--0.3987 °2
S-0.1134 Å °-0.2204 Å °0.0954 Å °0.0856 Å °0.0788 Å °0.0326 Å °0.0622 Å °0.0293 Å °0.0346 Å °

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