[English] 日本語
Yorodumi- PDB-3q8l: Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q8l | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with substrate 5'-flap DNA, SM3+, and K+ | ||||||
Components |
| ||||||
Keywords | HYDROLASE/DNA / helix-3 turn-helix / hydrophobic wedge / 3' flap binding site / hydrolase-DNA complex / DNA repair / replication / flap endonuclease / FEN / FEN1 / DNA / nuclease / 5' flap / ss-dsDNA junction / helix-2 turn-helix / H2TH / H3TH / divalent cation / metal helical gateway / cap / acid block / two metal mechanism / unpaired / 5' nuclease / human / long patch base excision repair | ||||||
Function / homology | Function and homology information positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / nucleic acid metabolic process / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / UV protection / Removal of the Flap Intermediate ...positive regulation of sister chromatid cohesion / flap endonuclease activity / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / nucleic acid metabolic process / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / 5'-3' exonuclease activity / UV protection / Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / HDR through MMEJ (alt-NHEJ) / exonuclease activity / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / base-excision repair, gap-filling / double-strand break repair via homologous recombination / memory / double-strand break repair / RNA-DNA hybrid ribonuclease activity / manganese ion binding / double-stranded DNA binding / endonuclease activity / DNA replication / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / DNA repair / nucleolus / magnesium ion binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / membrane / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.319 Å | ||||||
Authors | Tsutakawa, S.E. / Classen, S. / Chapados, B.R. / Arvai, A. / Finger, D.L. / Guenther, G. / Tomlinson, C.G. / Thompson, P. / Sarker, A.H. / Shen, B. ...Tsutakawa, S.E. / Classen, S. / Chapados, B.R. / Arvai, A. / Finger, D.L. / Guenther, G. / Tomlinson, C.G. / Thompson, P. / Sarker, A.H. / Shen, B. / Cooper, P.K. / Grasby, J.A. / Tainer, J.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2011 Title: Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily. Authors: Tsutakawa, S.E. / Classen, S. / Chapados, B.R. / Arvai, A.S. / Finger, L.D. / Guenther, G. / Tomlinson, C.G. / Thompson, P. / Sarker, A.H. / Shen, B. / Cooper, P.K. / Grasby, J.A. / Tainer, J.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3q8l.cif.gz | 207.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3q8l.ent.gz | 160.2 KB | Display | PDB format |
PDBx/mmJSON format | 3q8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q8l_validation.pdf.gz | 461.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3q8l_full_validation.pdf.gz | 469.3 KB | Display | |
Data in XML | 3q8l_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 3q8l_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/3q8l ftp://data.pdbj.org/pub/pdb/validation_reports/q8/3q8l | HTTPS FTP |
-Related structure data
Related structure data | 3q8kSC 3q8mC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38511.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FEN1, RAD2 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS References: UniProt: P39748, Hydrolases; Acting on ester bonds |
---|
-DNA chain , 3 types, 3 molecules DEF
#2: DNA chain | Mass: 5476.555 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized |
---|---|
#3: DNA chain | Mass: 3742.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized |
#4: DNA chain | Mass: 2058.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized |
-Non-polymers , 4 types, 409 molecules
#5: Chemical | ChemComp-SM / #6: Chemical | ChemComp-K / | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.11 % |
---|---|
Crystal grow | Temperature: 288 K / Method: vapor diffusion / pH: 7 Details: 17% mPEG 2k, 20% KCl, 0.5 mM Sm2(SO4)3, 50 mM Bis-Tris pH 7.0 and 5% Ethylene Glycol, vapor diffusion, temperature 288K |
-Data collection
Diffraction | Mean temperature: 90 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.116 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.116 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.319→91.12 Å / Num. all: 29199 / Num. obs: 29199 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.083 / Net I/σ(I): 8.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3Q8K Resolution: 2.319→20.481 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8711 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 19.9 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.572 Å2 / ksol: 0.338 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 187.75 Å2 / Biso mean: 60.0017 Å2 / Biso min: 9.69 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.319→20.481 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|