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- PDB-5u8g: DNA Polymerase Beta crystallized in PEG 400 -

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Basic information

Entry
Database: PDB / ID: 5u8g
TitleDNA Polymerase Beta crystallized in PEG 400
Components
  • DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
  • DNA (5'-D(*GP*TP*CP*GP*G)-3')
  • DNA polymerase beta
KeywordsTRANSFERASE / LYASE/DNA / DNA Polymerase / Lyase / DNA complex / LYASE-DNA complex
Function / homology
Function and homology information


Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / homeostasis of number of cells / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / homeostasis of number of cells / PCNA-Dependent Long Patch Base Excision Repair / POLB-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / base-excision repair, gap-filling / spleen development / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / spindle microtubule / response to gamma radiation / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA polymerase family X, beta-like / 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, beta-like / 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 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 / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / 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
DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.166 Å
AuthorsEckenroth, B.E. / Doublie, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA080830 United States
CitationJournal: Biochemistry / Year: 2017
Title: Remote Mutations Induce Functional Changes in Active Site Residues of Human DNA Polymerase beta.
Authors: Eckenroth, B.E. / Towle-Weicksel, J.B. / Nemec, A.A. / Murphy, D.L. / Sweasy, J.B. / Doublie, S.
History
DepositionDec 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification / _software.name
Revision 1.3Jan 16, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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 polymerase beta
T: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
P: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
D: DNA (5'-D(*GP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7737
Polymers47,6924
Non-polymers813
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-55 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.104, 78.659, 54.721
Angle α, β, γ (deg.)90.000, 104.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta /


Mass: 38241.672 Da / Num. of mol.: 1 / Fragment: DNA polymerase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 DE3
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 4853.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Primer Strand, 10mer / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Downstream Strand, 5mer / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*GP*TP*CP*GP*G)-3')


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Downstream Strand / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 269 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24% PEG 400, 30 mM potassium sodium tartrate, 1% 1,4-dioxane

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 11, 2013 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.166→14 Å / Num. obs: 45604 / % possible obs: 99.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 33.06 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.166-2.254.30.6220.738198.1
2.25-2.347.80.4820.901199.9
2.34-2.449.80.4160.9561100
2.44-2.5711.30.3350.9721100
2.57-2.7312.80.2570.9861100
2.73-2.9413.60.1960.9921100
2.94-3.2313.80.1350.9961100
3.23-3.6913.90.0990.9981100
3.69-4.6214.10.0830.9981100
4.62-1414.10.0620.9991100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ISB
Resolution: 2.166→13.68 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.27 / Details: refinement in Phenix with I+/I-
RfactorNum. reflection% reflection
Rfree0.2248 4537 9.95 %
Rwork0.1793 --
obs0.1839 45604 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.32 Å2 / Biso mean: 40.6452 Å2 / Biso min: 17.53 Å2
Refinement stepCycle: final / Resolution: 2.166→13.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2464 626 3 266 3359
Biso mean--33.47 43.62 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023228
X-RAY DIFFRACTIONf_angle_d0.4954485
X-RAY DIFFRACTIONf_chiral_restr0.021497
X-RAY DIFFRACTIONf_plane_restr0.002473
X-RAY DIFFRACTIONf_dihedral_angle_d17.5831249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1658-2.19030.35281200.3226974109471
2.1903-2.2160.37211420.32281247138990
2.216-2.24290.33811510.29411323147495
2.2429-2.27110.32441500.26271343149397
2.2711-2.30090.2731490.24991355150499
2.3009-2.33220.30551500.253314201570100
2.3322-2.36540.28781480.247113831531100
2.3654-2.40050.31521290.240714241553100
2.4005-2.43780.32761550.247813611516100
2.4378-2.47760.30611510.227114361587100
2.4776-2.520.27431410.222714071548100
2.52-2.56560.24691710.204613481519100
2.5656-2.61460.2551530.195513881541100
2.6146-2.66760.23551530.208914021555100
2.6676-2.72510.28151790.196613751554100
2.7251-2.7880.28831640.212713701534100
2.788-2.85710.29041400.204514231563100
2.8571-2.93360.24131240.207113911515100
2.9336-3.0190.271480.215214111559100
3.019-3.11540.29421470.197613751522100
3.1154-3.22530.28411880.184514041592100
3.2253-3.35260.20461650.174613691534100
3.3526-3.50280.20791040.172714001504100
3.5028-3.6840.19831590.150314221581100
3.684-3.90980.2111880.145513561544100
3.9098-4.20350.18711500.133614051555100
4.2035-4.61180.14331390.124113891528100
4.6118-5.24590.14861430.132413921535100
5.2459-6.48960.16231490.148313941543100
6.4896-13.68020.15321870.136413801567100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.1058-0.3230.06062.55260.19973.4540.0301-0.0563-0.2398-0.0725-0.0012-0.14650.2745-0.034-0.01570.2671-0.0140.02510.19130.01310.246631.7579-4.02759.4338
25.502-0.7085-0.44361.9010.35682.83360.0329-0.67680.0550.16230.0296-0.1233-0.10450.2757-0.04780.2384-0.00990.01150.26690.00850.209722.45099.885329.1753
35.73740.3683-0.41072.2444-0.16512.78160.1321-0.03970.0315-0.0306-0.05330.227-0.0655-0.2074-0.06880.1861-0.01180.00990.247-0.01050.2668-1.63948.568918.2635
41.26810.8874-0.86532.3081-1.15892.9134-0.57390.8639-0.3745-0.85040.7767-0.10870.4078-0.3201-0.15810.457-0.18490.01640.754-0.16160.39163.92887.8586-4.7032
59.11990.3002-3.8166.1994-0.49677.3308-0.0084-0.07140.76060.11420.3354-0.0405-0.2870.5872-0.33750.44760.02530.01310.2659-0.01220.296731.709713.9751-3.1309
61.7230.2932-0.18543.42280.8562.01550.14560.0220.23480.3149-0.2656-0.43960.14560.03270.06470.3606-0.0053-0.00890.20210.03920.410817.10724.321115.1216
72.14270.12-0.37668.31711.20352.71550.2522-0.180.269-0.6758-0.4809-0.0322-0.3249-0.21660.23190.3467-0.0097-0.0470.2882-0.03650.312717.624125.611716.0033
83.42670.5841-1.0774.8285-1.34124.00690.25050.74480.31080.0170.16620.2093-0.2288-0.2516-0.31430.38160.0375-0.01010.30250.06720.277731.31086.2424-4.2202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 89 )A11 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 150 )A90 - 150
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 260 )A151 - 260
4X-RAY DIFFRACTION4chain 'A' and (resid 261 through 335 )A261 - 335
5X-RAY DIFFRACTION5chain 'T' and (resid 1 through 5 )T1 - 5
6X-RAY DIFFRACTION6chain 'T' and (resid 6 through 16 )T6 - 16
7X-RAY DIFFRACTION7chain 'P' and (resid 1 through 10 )P1 - 10
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 5 )D1 - 5

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