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Yorodumi- PDB-5cwr: Crystal Structure of human DNA polymerase lambda L431A mutant in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cwr | ||||||
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Title | Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Polymerase lambda / TRANSFERASE / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / Nonhomologous End-Joining (NHEJ) / nucleotide-excision repair / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / Nonhomologous End-Joining (NHEJ) / nucleotide-excision repair / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Liu, M.S. / Tsai, M.D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Structural Mechanism for the Fidelity Modulation of DNA Polymerase lambda Authors: Liu, M.S. / Tsai, H.Y. / Liu, X.X. / Ho, M.C. / Wu, W.J. / Tsai, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cwr.cif.gz | 174.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cwr.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 5cwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cwr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5cwr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5cwr_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 5cwr_validation.cif.gz | 42.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cw/5cwr ftp://data.pdbj.org/pub/pdb/validation_reports/cw/5cwr | HTTPS FTP |
-Related structure data
Related structure data | 4xq8C 4xrhC 5ca7C 5cb1C 5chgC 5cj7C 5cp2C 5cr0C 5ddmC 5ddyC 5dkwC 3mgiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36507.617 Da / Num. of mol.: 2 / Fragment: UNP residues 250-575 / Mutation: L431A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UGP5, DNA-directed DNA polymerase |
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-DNA chain , 3 types, 6 molecules TFPEDC
#2: DNA chain | Mass: 3390.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CGGCGGTACTG / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 1793.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: DNA chain | Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 313 molecules
#5: Chemical | #6: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 69.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.15 M Potassium Bromide, 30% Polyethylene Glycol Monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 27, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→30 Å / Num. obs: 41766 / % possible obs: 98.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.042 / Rrim(I) all: 0.1 / Χ2: 1.323 / Net I/av σ(I): 19.422 / Net I/σ(I): 9.1 / Num. measured all: 228026 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MGI Resolution: 2.5→28.123 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28.123 Å
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Refine LS restraints |
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LS refinement shell |
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