+Open data
-Basic information
Entry | Database: PDB / ID: 7rss | ||||||
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Title | Kod-RI incorporating DNA, n+2 | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Polymerase / TRANSFERASE / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermococcus kodakarensis (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Hajjar, M. / Chim, N. / Chaput, J.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Crystallographic analysis of engineered polymerases synthesizing phosphonomethylthreosyl nucleic acid. Authors: Hajjar, M. / Chim, N. / Liu, C. / Herdewijn, P. / Chaput, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rss.cif.gz | 358.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rss.ent.gz | 287.5 KB | Display | PDB format |
PDBx/mmJSON format | 7rss.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rss_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 7rss_full_validation.pdf.gz | 445.9 KB | Display | |
Data in XML | 7rss_validation.xml.gz | 28.1 KB | Display | |
Data in CIF | 7rss_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/7rss ftp://data.pdbj.org/pub/pdb/validation_reports/rs/7rss | HTTPS FTP |
-Related structure data
Related structure data | 7rsrC 7tqwC 5vu9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 90130.617 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWU9, DNA-directed DNA polymerase |
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#2: DNA chain | Mass: 4898.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 3985.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate, sodium citrate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→57.03 Å / Num. obs: 30746 / % possible obs: 99.36 % / Redundancy: 2 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.02637 / Rpim(I) all: 0.02637 / Rrim(I) all: 0.03729 / Net I/σ(I): 13.14 |
Reflection shell | Resolution: 2.71→2.807 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1368 / Num. unique obs: 3037 / CC1/2: 0.949 / CC star: 0.987 / Rpim(I) all: 0.1368 / Rrim(I) all: 0.1934 / Net I/σ(I) obs: 4.74 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VU9 Resolution: 2.71→62.087 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.83 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166.09 Å2 / Biso mean: 52.3407 Å2 / Biso min: 19.29 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.71→62.087 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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