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- PDB-7kt9: DNA Polymerase Mu, 8-oxodGTP:At Product State Ternary Complex, 50... -

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Basic information

Entry
Database: PDB / ID: 7kt9
TitleDNA Polymerase Mu, 8-oxodGTP:At Product State Ternary Complex, 50 mM Mg2+ (960min)
Components
  • DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
KeywordsREPLICATION / Time-Lapse Crystallography / Oxidized Nucleotide Insertion / Double Strand Break Repair
Function / homology
Function and homology information


Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family ...DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / GLYCOLIC ACID / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.482 Å
AuthorsJamsen, J.A. / Wilson, S.H.
Funding support United States, Japan, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050158 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050161 United States
Japan Society for the Promotion of Science (JSPS)16K16195 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide.
Authors: Jamsen, J.A. / Sassa, A. / Shock, D.D. / Beard, W.A. / Wilson, S.H.
History
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed DNA/RNA polymerase mu
T: DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
P: DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,28414
Polymers45,5234
Non-polymers76110
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-47 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.283, 68.316, 111.407
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA-directed DNA/RNA polymerase mu / Pol Mu / Terminal transferase


Mass: 40054.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Plasmid: pGEXM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NP87, DNA-directed DNA polymerase

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DNA chain , 3 types, 3 molecules TPD

#2: DNA chain DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')


Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')


Mass: 1536.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*GP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 8 types, 467 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID / Glycolic acid


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.18 % / Mosaicity: 0.157 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 85-90mM HEPES pH 7.5, 17-18% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 76825 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.056 / Rrim(I) all: 0.138 / Χ2: 1.075 / Net I/σ(I): 12 / Num. measured all: 444209
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.48-1.515.90.57138000.8480.2520.6261.06499.9
1.51-1.535.90.537890.8780.2210.5481.14499.8
1.53-1.5660.43737710.8970.1920.4791.1399.8
1.56-1.595.90.36438210.9220.1620.3991.15499.9
1.59-1.635.80.31138070.9360.1390.3411.13399.7
1.63-1.675.70.27137830.9550.1230.2991.11599.8
1.67-1.715.50.23638250.9550.110.2611.1199.4
1.71-1.754.90.237970.9630.0980.2241.07299.8
1.75-1.815.80.18737950.9710.0830.2061.097100
1.81-1.866.20.17138390.9770.0730.1861.12599.9
1.86-1.936.10.15638110.9790.0670.1711.093100
1.93-2.0160.14438630.980.0630.1571.122100
2.01-2.15.90.13838230.9770.060.1511.06699.7
2.1-2.215.80.12738240.9810.0570.141.09999.6
2.21-2.355.50.12238300.980.0560.1341.04499.4
2.35-2.5350.11538570.9780.0550.1280.98798.9
2.53-2.796.30.1238480.9820.0510.131.0599.8
2.79-3.196.20.11839220.980.0510.1291.027100
3.19-4.025.90.11339540.9790.050.1240.93199.8
4.02-505.40.11340660.9780.0520.1250.92298.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.15.2-3472refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M04

4m04


Resolution: 1.482→45.201 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1755 3838 5 %
Rwork0.1552 72921 -
obs0.1562 76759 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.35 Å2 / Biso mean: 22.8378 Å2 / Biso min: 8.55 Å2
Refinement stepCycle: final / Resolution: 1.482→45.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 367 25 465 3403
Biso mean--29.72 33.65 -
Num. residues----344
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.482-1.50070.23351360.2107259798
1.5007-1.52050.20791420.19482695100
1.5205-1.54130.19421400.18552658100
1.5413-1.56330.19821410.18542665100
1.5633-1.58670.19751420.17512700100
1.5867-1.61140.20951390.16872640100
1.6114-1.63790.19221430.1632694100
1.6379-1.66610.17691400.15952684100
1.6661-1.69640.1991420.15442668100
1.6964-1.7290.20381400.15392672100
1.729-1.76430.18821410.15432672100
1.7643-1.80270.15821410.15172689100
1.8027-1.84460.191420.14842703100
1.8446-1.89080.18871420.1482717100
1.8908-1.94190.18181380.15222702100
1.9419-1.9990.17581470.15322655100
1.999-2.06360.18811400.15122709100
2.0636-2.13730.18171400.1493270399
2.1373-2.22290.17171400.14332713100
2.2229-2.3240.17641460.1457268699
2.324-2.44660.15241420.1389267399
2.4466-2.59980.17081430.144270899
2.5998-2.80050.16441420.15382719100
2.8005-3.08230.18251450.16072759100
3.0823-3.52820.15961460.15512776100
3.5282-4.44450.15611460.1434277699
4.4445-45.2010.18651520.1745288898
Refinement TLS params.Method: refined / Origin x: 2.8445 Å / Origin y: -4.2832 Å / Origin z: -11.3322 Å
111213212223313233
T0.1139 Å20.0031 Å2-0.0016 Å2-0.1132 Å20.0118 Å2--0.0861 Å2
L1.121 °2-0.2086 °2-0.1268 °2-0.7321 °20.0721 °2--0.6318 °2
S0.0454 Å °0.103 Å °0.0681 Å °-0.0365 Å °-0.0324 Å °-0.0395 Å °-0.0042 Å °0.0275 Å °0.0045 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA137 - 494
2X-RAY DIFFRACTION1allA501
3X-RAY DIFFRACTION1allT1 - 9
4X-RAY DIFFRACTION1allP1 - 5
5X-RAY DIFFRACTION1allD1 - 4
6X-RAY DIFFRACTION1allE1 - 2
7X-RAY DIFFRACTION1allB1 - 4
8X-RAY DIFFRACTION1allC1
9X-RAY DIFFRACTION1allG1
10X-RAY DIFFRACTION1allH1
11X-RAY DIFFRACTION1allS2 - 530
12X-RAY DIFFRACTION1allF1

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