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- PDB-4eyi: Human DNA polymerase iota incorporating dATP opposite N-(deoxygua... -

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Basic information

Entry
Database: PDB / ID: 4eyi
TitleHuman DNA polymerase iota incorporating dATP opposite N-(deoxyguanosin-8-yl)-1-aminopyrene lesion
Components
  • DNA polymerase iota
  • DNA primer
  • DNA template
KeywordsTRANSFERASE/DNA / DNA polymerase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


translesion synthesis / error-prone 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 ...translesion synthesis / error-prone 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
HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb 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 ...HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb 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
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKirouac, K. / Ling, H.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Replication of a carcinogenic nitropyrene DNA lesion by human Y-family DNA polymerase.
Authors: Kirouac, K.N. / Basu, A.K. / Ling, H.
History
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _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
B: DNA polymerase iota
T: DNA template
P: DNA primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3737
Polymers51,8093
Non-polymers5644
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-54 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.850, 98.850, 194.203
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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Protein , 1 types, 1 molecules B

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


Mass: 47027.344 Da / Num. of mol.: 1 / Fragment: UNP residues 26-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLI, RAD30B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UNA4, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA template


Mass: 2673.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized
#3: DNA chain DNA primer


Mass: 2107.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized

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Non-polymers , 3 types, 32 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 5000MME, 0.2 M NH4SO4, 0.1M MES pH 6.5, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.9→32.356 Å / Num. all: 13665 / Num. obs: 12929 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→32.356 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2637 1028 7.95 %
Rwork0.2179 --
obs0.2216 12929 98.85 %
all-13665 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.683 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8847 Å2-0 Å20 Å2
2---1.8847 Å20 Å2
3---3.7695 Å2
Refinement stepCycle: LAST / Resolution: 2.9→32.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2946 326 33 28 3333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063393
X-RAY DIFFRACTIONf_angle_d1.144657
X-RAY DIFFRACTIONf_dihedral_angle_d19.9821304
X-RAY DIFFRACTIONf_chiral_restr0.07541
X-RAY DIFFRACTIONf_plane_restr0.004536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9003-3.05310.36461410.33691659X-RAY DIFFRACTION99
3.0531-3.24420.35161470.27161656X-RAY DIFFRACTION100
3.2442-3.49440.30451410.24331690X-RAY DIFFRACTION100
3.4944-3.84560.31441530.22661676X-RAY DIFFRACTION99
3.8456-4.40080.24141360.19181703X-RAY DIFFRACTION99
4.4008-5.54010.22421510.19511711X-RAY DIFFRACTION98
5.5401-32.35830.24061590.20771806X-RAY DIFFRACTION97
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)
10.67640.0226-0.14471.74650.69460.9783-0.1959-0.07870.01640.3358-0.30930.19540.502-0.4836-00.516-0.18350.04780.6304-0.11540.5091-0.378816.966722.2549
20.90440.36561.04940.5164-0.09790.8347-0.0788-0.03130.42980.0097-0.0927-0.37480.22550.202700.5016-0.0306-0.0630.48760.15130.597221.545522.2397.2744
30.1341-0.10240.0680.34720.52360.23550.03570.1005-0.0969-0.048-0.2683-0.22150.1869-0.034600.53450.0467-0.0450.48980.06720.532516.150815.08331.2059
40.59160.05961.17060.91320.09140.9993-0.0641-0.0840.0669-0.1583-0.14240.0657-0.05810.0084-00.52520.015-0.15550.49290.0130.55252.754632.52130.0988
50.3751-0.15110.47291.76050.90192.37360.7461-0.2865-0.11490.5167-0.3243-0.13580.3866-0.5639-00.87-0.30580.02321.1774-0.05190.76223.904144.238333.8333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain B and resid 27:105)
2X-RAY DIFFRACTION2(chain B and resid 106:152)
3X-RAY DIFFRACTION3(chain B and resid 153:194)
4X-RAY DIFFRACTION4(chain B and resid 195:301)
5X-RAY DIFFRACTION5(chain B and resid 302:416)

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