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- PDB-5kt5: Teranry complex of human DNA polymerase iota R96G inserting dCMPN... -

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Basic information

Entry
Database: PDB / ID: 5kt5
TitleTeranry complex of human DNA polymerase iota R96G inserting dCMPNPP opposite template G in the presence of Mn2+
Components
  • DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3')
  • DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3')
  • DNA polymerase iotaPOLI
KeywordsTRANSFERASE / DNA polymerase / POLI / R96G / manganese
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
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
Chem-0KX / : / DNA / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.798 Å
AuthorsChoi, J.Y. / Patra, A. / Yeom, M. / Lee, Y.S. / Zhang, Q. / Egli, M. / Guengerich, F.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES010375 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01 ES010546 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase iota.
Authors: Choi, J.Y. / Patra, A. / Yeom, M. / Lee, Y.S. / Zhang, Q. / Egli, M. / Guengerich, F.P.
History
DepositionJul 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
T: DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3')
P: DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3')
A: DNA polymerase iota
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3536
Polymers54,7773
Non-polymers5763
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-33 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.111, 98.111, 202.761
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 DNA (5'-D(*CP*TP*GP*GP*GP*GP*TP*CP*CP*T)-3')


Mass: 3051.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3')


Mass: 2107.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules A

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


Mass: 49617.875 Da / Num. of mol.: 1 / Fragment: UNP residues 1-445
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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Non-polymers , 3 types, 13 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-0KX / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine


Mass: 466.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17N4O12P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 18% PEG MME 5000, 0.1M MES buffer, 0.3M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.798→42.483 Å / Num. obs: 14993 / % possible obs: 99.9 % / Redundancy: 21 % / Biso Wilson estimate: 53.66 Å2 / Rmerge(I) obs: 0.117 / Net I/av σ(I): 30.125 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.8-2.8521.30.8420.959199.9
2.85-2.921.20.8120.945199.7
2.9-2.9621.60.5840.97199.9
2.96-3.0221.60.5490.971199.9
3.02-3.0821.50.4610.979199.7
3.08-3.1521.70.3530.987199.9
3.15-3.2321.60.2680.993199.9
3.23-3.3221.50.2220.9951100
3.32-3.4221.60.1720.997199.9
3.42-3.5321.40.1760.9961100
3.53-3.6521.40.140.9981100
3.65-3.821.10.1220.9981100
3.8-3.9721.40.1060.9991100
3.97-4.1821.10.090.9991100
4.18-4.4421.10.080.9991100
4.44-4.7920.90.0790.9991100
4.79-5.2720.70.0820.9991100
5.27-6.0320.50.0780.999199.9
6.03-7.5919.90.0580.999199.9
7.59-5017.50.0470.999199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.798→42.483 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.73
RfactorNum. reflection% reflection
Rfree0.2664 781 5.24 %
Rwork0.2236 --
obs0.2258 14915 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.07 Å2 / Biso mean: 51.4303 Å2 / Biso min: 12.49 Å2
Refinement stepCycle: final / Resolution: 2.798→42.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2887 345 30 10 3272
Biso mean--31.65 34.06 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033340
X-RAY DIFFRACTIONf_angle_d0.6294597
X-RAY DIFFRACTIONf_chiral_restr0.041546
X-RAY DIFFRACTIONf_plane_restr0.004532
X-RAY DIFFRACTIONf_dihedral_angle_d15.8421980
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.798-2.97290.38261090.276823152424100
2.9729-3.20230.30311400.264922692409100
3.2023-3.52450.26961370.23323112448100
3.5245-4.03410.29431510.225923072458100
4.0341-5.08120.25861030.200824022505100
5.0812-42.48820.21221410.21132530267199

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