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- PDB-2dpj: structure of hPoli with DNA and dTTP -

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Basic information

Entry
Database: PDB / ID: 2dpj
Titlestructure of hPoli with DNA and dTTP
Components
  • 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'
  • 5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3'
  • DNA polymerase iota
KeywordsTRANSFERASE/DNA / DNA dependent DNA Polymerase / ethenodA adduct / lesion bypass / dTTP / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck ...error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nuclear speck / DNA repair / nucleoplasm / metal ion binding
Similarity search - Function
DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain ...DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNair, D.T. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Hoogsteen base pair formation promotes synthesis opposite the 1,N(6)-ethenodeoxyadenosine lesion by human DNA polymerase iota.
Authors: Nair, D.T. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionMay 12, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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 / struct_conn_type / struct_site
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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'
T: 5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3'
A: DNA polymerase iota
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4206
Polymers51,8903
Non-polymers5313
Water2,288127
1
P: 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'
T: 5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3'
A: DNA polymerase iota
hetero molecules

P: 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'
T: 5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3'
A: DNA polymerase iota
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,84112
Polymers103,7796
Non-polymers1,0626
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Unit cell
Length a, b, c (Å)98.059, 98.059, 203.102
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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DNA chain , 2 types, 2 molecules PT

#1: DNA chain 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'


Mass: 2091.414 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*(EDA)P*GP*GP*GP*TP*CP*CP*T)-3'


Mass: 2770.830 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase iota / RAD30 homolog B / Eta2


Mass: 47027.344 Da / Num. of mol.: 1 / Fragment: residues 1-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLI, RAD30B / Plasmid: pBJ941 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): Bj5464 / References: UniProt: Q9UNA4, DNA-directed DNA polymerase

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Non-polymers , 3 types, 130 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 5K MME, 0.4M Ammonium Sulfate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 5K MME11
2Ammonium Sulfate11
3MES11
4HOH11
5PEG 5K MME12
6Ammonium Sulfate12
7MES12
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 26535 / % possible obs: 99.3 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 45.6
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 8.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ALZ

2alz


Resolution: 2.3→36.76 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.707 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: the structure was refined also with CNS1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1964 7.9 %RANDOM
Rwork0.23805 ---
obs0.2412 22903 93.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.591 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.3 Å20 Å2
2--0.61 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2876 323 31 127 3357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0223306
X-RAY DIFFRACTIONr_angle_refined_deg2.8652.1134531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6125370
X-RAY DIFFRACTIONr_chiral_restr0.1970.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022317
X-RAY DIFFRACTIONr_nbd_refined0.30.21339
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3650.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.310.28
X-RAY DIFFRACTIONr_mcbond_it1.7961.51860
X-RAY DIFFRACTIONr_mcangle_it3.14322997
X-RAY DIFFRACTIONr_scbond_it4.30731446
X-RAY DIFFRACTIONr_scangle_it6.1794.51534
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 121
Rwork0.278 1527
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.11250.1630.08520.70210.47791.6540.05150.0174-0.0296-0.0149-0.09040.03050.09510.1960.03890.35520.0205-0.02930.35870.00460.26516.174216.65316.0704
21.6038-0.1424-0.7813.07090.7514.23750.1035-0.0819-0.13730.1821-0.1590.48050.4428-0.37910.05550.3333-0.1790.06790.327-0.04180.3458-5.083516.225323.7223
33.6034-0.63152.87642.16490.77453.488-0.5834-0.0730.8525-0.1225-0.1885-0.1288-0.2702-0.16650.77190.32690.006-0.21840.2564-0.03040.47780.203635.5023-3.3046
42.90951.9998-1.19956.85020.08943.90230.9063-0.23840.41461.132-0.670.8768-0.29410.272-0.23630.4633-0.27120.26290.1735-0.20930.35787.049741.333232.9066
51.3952-0.0858-1.13981.656-0.47850.55790.0607-0.08150.578-0.0049-0.08860.51450.01340.18910.02790.342-0.1273-0.03940.2985-0.04520.49674.332136.88917.2732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC26 - 3726 - 37
2X-RAY DIFFRACTION1AC99 - 22499 - 224
3X-RAY DIFFRACTION2AC38 - 9838 - 98
4X-RAY DIFFRACTION3AC225 - 287225 - 287
5X-RAY DIFFRACTION4AC298 - 414298 - 414
6X-RAY DIFFRACTION5TB839 - 8471 - 9
7X-RAY DIFFRACTION5PA867 - 8731 - 7
8X-RAY DIFFRACTION5AF8751
9X-RAY DIFFRACTION5AD - E871 - 8721

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