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- PDB-5tyg: DNA Polymerase Mu Product Complex, 10 mM Mg2+ (960 min) -

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Basic information

Entry
Database: PDB / ID: 5tyg
TitleDNA Polymerase Mu Product Complex, 10 mM Mg2+ (960 min)
Components
  • DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*AP*T)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
KeywordsTransferase/DNA / Time-Lapse Crystallography / Product Metal / DNA Polymerase Mu / Double Strand Break Repair / Transferase-DNA complex
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 / nucleus / metal ion binding
Similarity search - Function
DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / 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-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / 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 family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
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)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.726 Å
AuthorsJamsen, J.A. / Wilson, S.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050158 United States
CitationJournal: Nat Commun / Year: 2017
Title: Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.
Authors: Jamsen, J.A. / Beard, W.A. / Pedersen, L.C. / Shock, D.D. / Moon, A.F. / Krahn, J.M. / Bebenek, K. / Kunkel, T.A. / Wilson, S.H.
History
DepositionNov 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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*T)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,20713
Polymers45,4824
Non-polymers7259
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-43 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.998, 68.534, 110.747
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 / Fragment: UNP residues 132-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Plasmid: pGEXM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CodonPlus-RIL / 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.) unidentified (others)
#3: DNA chain DNA (5'-D(*CP*GP*TP*AP*T)-3')


Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) unidentified (others)
#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.) unidentified (others)

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Non-polymers , 7 types, 394 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#10: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.96 %
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
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 48725 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 24.59 Å2 / Rmerge(I) obs: 0.055 / Net I/av σ(I): 36.814 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.73-1.767.30.9090.7531100
1.76-1.797.30.7590.8171100
1.79-1.837.30.6190.8791100
1.83-1.867.40.5160.9121100
1.86-1.97.40.430.9281100
1.9-1.957.40.3570.9541100
1.95-27.40.2890.9671100
2-2.057.40.2410.981100
2.05-2.117.40.1990.9831100
2.11-2.187.40.1610.991100
2.18-2.267.40.1390.9911100
2.26-2.357.40.1120.9941100
2.35-2.457.40.0920.9961100
2.45-2.587.40.0780.9971100
2.58-2.757.40.0690.9981100
2.75-2.967.40.0650.9971100
2.96-3.267.30.0450.9991100
3.26-3.737.30.0310.9991100
3.73-4.697.20.0240.9991100
4.69-506.90.0230.999199.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data collection
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.726→34.989 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 17.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1853 2434 5 %
Rwork0.1547 46224 -
obs0.1562 48658 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.99 Å2 / Biso mean: 32.5416 Å2 / Biso min: 13.87 Å2
Refinement stepCycle: final / Resolution: 1.726→34.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 364 25 393 3356
Biso mean--41.45 40.09 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073304
X-RAY DIFFRACTIONf_angle_d0.8764584
X-RAY DIFFRACTIONf_chiral_restr0.052498
X-RAY DIFFRACTIONf_plane_restr0.006542
X-RAY DIFFRACTIONf_dihedral_angle_d10.0841721
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7259-1.76110.28471370.23692600273796
1.7611-1.79940.24631400.205326652805100
1.7994-1.84130.2011410.190426882829100
1.8413-1.88730.22311420.180626932835100
1.8873-1.93840.2331380.174527092847100
1.9384-1.99540.1971460.164126802826100
1.9954-2.05980.23761390.16426892828100
2.0598-2.13340.20541450.152827162861100
2.1334-2.21880.19441420.151727122854100
2.2188-2.31980.19191430.142226862829100
2.3198-2.4420.19251440.143627102854100
2.442-2.5950.18071420.149927312873100
2.595-2.79530.18591440.162327132857100
2.7953-3.07640.19421450.162227482893100
3.0764-3.52120.18111450.151227752920100
3.5212-4.4350.13691450.129927832928100
4.435-34.99630.1861560.159929263082100
Refinement TLS params.Method: refined / Origin x: 2.9316 Å / Origin y: -4.191 Å / Origin z: -11.5595 Å
111213212223313233
T0.1815 Å20.0064 Å2-0.0029 Å2-0.1801 Å20.0153 Å2--0.1193 Å2
L1.3409 °2-0.2973 °2-0.1831 °2-0.9358 °20.1401 °2--0.684 °2
S0.0593 Å °0.1317 Å °0.0562 Å °-0.056 Å °-0.0435 Å °-0.0386 Å °0.0201 Å °0.0296 Å °-0.0153 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA137 - 494
2X-RAY DIFFRACTION1allT1 - 9
3X-RAY DIFFRACTION1allP1 - 5
4X-RAY DIFFRACTION1allD1 - 4
5X-RAY DIFFRACTION1allB2
6X-RAY DIFFRACTION1allC1 - 2
7X-RAY DIFFRACTION1allF1
8X-RAY DIFFRACTION1allG1 - 4
9X-RAY DIFFRACTION1allH1
10X-RAY DIFFRACTION1allS1 - 504
11X-RAY DIFFRACTION1allE1

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