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- SASDCN5: Vaccinia virus DNA polymerase (DNA polymerase E9, E9) -

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Open data


ID or keywords:

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Basic information

Entry
Database: SASBDB / ID: SASDCN5
SampleVaccinia virus DNA polymerase
  • DNA polymerase E9 (protein), E9, Vaccinia virus (strain Copenhagen)
Function / homology
Function and homology information


viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA recombination / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain ...DNA-directed DNA polymerase, family B, viral insert domain / DNA polymerase B exonuclease, N-terminal / DNA polymerase family B viral insert / DNA polymerase family B exonuclease domain, N-terminal / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesVaccinia virus (strain Copenhagen)
CitationDate: 2017 Dec
Title: The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding
Authors: Tarbouriech N / Ducournau C / Hutin S / Mas P / Man P / Forest E / Hart D / Peyrefitte C / Burmeister W
Contact author
  • Wim Burmeister (IBS, Institut de Biologie Structurale, Grenoble, France)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

Model #1358
Type: atomic / Software: (1.6) / Radius of dummy atoms: 1.70 A / Symmetry: none / Comment: Calculated scattering curve of protein / Chi-square value: 0.569
Search similar-shape structures of this assembly by Omokage search (details)

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Sample

SampleName: Vaccinia virus DNA polymerase
BufferName: 20 mM Tris HCl, 100 mM NaCl, 4 mM DTT / pH: 7
Entity #729Name: E9 / Type: protein / Description: DNA polymerase E9 / Formula weight: 117.242 / Num. of mol.: 1 / Source: Vaccinia virus (strain Copenhagen) / References: UniProt: P20509
Sequence: GAMDPDVRCI NWFESHGENR FLYLKSRCRN GETVFIRFPH YFYYVVTDEI YQSLSPPPFN ARPLGKMRTI DIDETISYNL DIKDRKCSVA DMWLIEEPKK RSIQNATMDE FLNISWFYIS NGISPDGCYS LDEQYLTKIN NGCYHCDDPR NCFAKKIPRF DIPRSYLFLD ...Sequence:
GAMDPDVRCI NWFESHGENR FLYLKSRCRN GETVFIRFPH YFYYVVTDEI YQSLSPPPFN ARPLGKMRTI DIDETISYNL DIKDRKCSVA DMWLIEEPKK RSIQNATMDE FLNISWFYIS NGISPDGCYS LDEQYLTKIN NGCYHCDDPR NCFAKKIPRF DIPRSYLFLD IECHFDKKFP SVFINPISHT SYCYIDLSGK RLLFTLINEE MLTEQEIQEA VDRGCLRIQS LMEMDYEREL VLCSEIVLLR IAKQLLELTF DYVVTFNGHN FDLRYITNRL ELLTGEKIIF RSPDKKEAVH LCIYERNQSS HKGVGGMANT TFHVNNNNGT IFFDLYSFIQ KSEKLDSYKL DSISKNAFSC MGKVLNRGVR EMTFIGDDTT DAKGKAAAFA KVLTTGNYVT VDEDIICKVI RKDIWENGFK VVLLCPTLPN DTYKLSFGKD DVDLAQMYKD YNLNIALDMA RYCIHDACLC QYLWEYYGVE TKTDAGASTY VLPQSMVFEY RASTVIKGPL LKLLLETKTI LVRSETKQKF PYEGGKVFAP KQKMFSNNVL IFDYNSLYPN VCIFGNLSPE TLVGVVVSTN RLEEEINNQL LLQKYPPPRY ITVHCEPRLP NLISEIAIFD RSIEGTIPRL LRTFLAERAR YKKMLKQATS STEKAIYDSM QYTYKIVANS VYGLMGFRNS ALYSYASAKS CTSIGRRMIL YLESVLNGAE LSNGMLRFAN PLSNPFYMDD RDINPIVKTS LPIDYRFRFR SVYGDTDSVF TEIDSQDVDK SIEIAKELER LINNRVLFNN FKIEFEAVYK NLIMQSKKKY TTMKYSASSN SKSVPERINK GTSETRRDVS KFHKNMIKTY KTRLSEMLSE GRMNSNQVCI DILRSLETDL RSEFDSRSSP LELFMLSRMH HSNYKSADNP NMYLVTEYNK NNPETIELGE RYYFAYICPA NVPWTKKLVN IKTYETIIDR SFKLGSDQRI FYEVYFKRLT SEIVNLLDNK VLCISFFERM FGSKPTFYEA

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Experimental information

BeamInstrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.0992 Å / Dist. spec. to detc.: 2.864 mm
DetectorName: Pilatus 1M
Scan
Title: Vaccinia virus DNA polymerase / Measurement date: Nov 27, 2014 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 900 / Unit: 1/nm /
MinMax
Q0.079 2.6381
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 459 /
MinMax
Q0.169073 2.33958
P(R) point1 459
R0 12
Result
Type of curve: other /
ExperimentalPorod
MW117 kDa117 kDa
Volume-202 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I027 0.09 19.97 0.05
Radius of gyration, Rg3.55 nm0.01 3.9 nm0.2

MinMax
D-12
Guinier point1 45

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