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- PDB-1zet: X-ray data do not support hoogsteen base-pairing during replicati... -

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Basic information

Entry
Database: PDB / ID: 1zet
TitleX-ray data do not support hoogsteen base-pairing during replication by human polymerase iota
Components
  • 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*(DOC))-3'
  • 5'-D(P*AP*GP*GP*GP*(BRU)P*CP*CP*(BRU)P*(BRU)P*CP*CP*CP*CP*C)-3'
  • Polymerase (DNA directed) iota
KeywordsREPLICATION/DNA / PROTEIN / DNA / DTTP / STATISTICAL DYAD / REPLICATION-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 (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsWang, J.
CitationJournal: Nature / Year: 2004
Title: Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing.
Authors: Nair, D.T. / Johnson, R.E. / Prakash, S. / Prakash, L. / Aggarwal, A.K.
History
DepositionApr 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 28, 2011Group: Other
Revision 1.4Feb 14, 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_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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 1ZET REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1T3NSF ORIGINAL DATA ...THIS ENTRY 1ZET REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN R1T3NSF ORIGINAL DATA DETERMINED BY AUTHOR: D.T.NAIR,R.E.JOHNSON,S.PRAKASH,L.PRAKASH,A.K.AGGARWAL

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
T: 5'-D(P*AP*GP*GP*GP*(BRU)P*CP*CP*(BRU)P*(BRU)P*CP*CP*CP*CP*C)-3'
P: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*(DOC))-3'
A: Polymerase (DNA directed) iota
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8235
Polymers52,3173
Non-polymers5062
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.831, 98.831, 202.755
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 TP

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


Mass: 4387.327 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*(DOC))-3'


Mass: 4050.649 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#3: Protein Polymerase (DNA directed) iota


Mass: 43878.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLI / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 21619716, UniProt: Q9UNA4*PLUS

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Non-polymers , 3 types, 170 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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.: 168 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.65 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1T3N.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementResolution: 2.3→39.43 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 559823.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THIS ENTRY REFLECTS AN ALTERNATIVE MODELING OF X-RAY DATA R1T3NSF
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1529 5.8 %RANDOM
Rwork0.261 ---
obs0.261 26413 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.6238 Å2 / ksol: 0.326022 e/Å3
Displacement parametersBiso mean: 71.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.9 Å23.74 Å20 Å2
2--6.9 Å20 Å2
3----13.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 550 30 168 3816
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it6.061.5
X-RAY DIFFRACTIONc_mcangle_it7.672
X-RAY DIFFRACTIONc_scbond_it8.782
X-RAY DIFFRACTIONc_scangle_it10.412.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 252 6 %
Rwork0.292 3933 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TTP.PARDNA-RNA-BRU.TOP
X-RAY DIFFRACTION3DNA-RNA_REP-BRU.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMTTP.TOP
X-RAY DIFFRACTION5WATER_REP.PARAMION.TOP

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