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- PDB-2alz: Ternary Complex of hPoli with DNA and dCTP -

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Basic information

Entry
Database: PDB / ID: 2alz
TitleTernary Complex of hPoli with DNA and dCTP
Components
  • 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'
  • 5'-D(*TP*GP*GP*GP*GP*TP*CP*CP*T)-3'
  • DNA polymerase iota
KeywordsTransferase/DNA / right handed / DNA polymerase / ternary complex / template G. incoming dCTP / Hoogsteen base pair / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNair, D.T. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
CitationJournal: Structure / Year: 2005
Title: Human DNA Polymerase iota Incorporates dCTP Opposite Template G via a G.C+ Hoogsteen Base Pair.
Authors: Nair, D.T. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionAug 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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
T: 5'-D(*TP*GP*GP*GP*GP*TP*CP*CP*T)-3'
P: 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'
A: DNA polymerase iota
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4076
Polymers48,8913
Non-polymers5163
Water1,42379
1
T: 5'-D(*TP*GP*GP*GP*GP*TP*CP*CP*T)-3'
P: 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'
A: DNA polymerase iota
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)98,81412
Polymers97,7836
Non-polymers1,0326
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)98.114, 98.114, 202.823
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(*TP*GP*GP*GP*GP*TP*CP*CP*T)-3'


Mass: 2762.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template
#2: DNA chain 5'-D(*AP*GP*GP*AP*CP*CP*(DOC))-3'


Mass: 2091.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA primer

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Protein , 1 types, 1 molecules A

#3: Protein DNA polymerase iota / E.C.2.7.7.7 / RAD30 homolog B / Eta2


Mass: 44037.047 Da / Num. of mol.: 1
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, 82 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.7 Å3/Da / Density % sol: 54.2 %
Crystal growpH: 6.5
Details: 16% PEG 5K MME, 0.4 M Ammonium Sulfate, 0.1 M MES buffer, pH 6.5, hanging drop, pH 6.50

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.072
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 20339 / % possible obs: 99 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 6.6 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T3N

1t3n


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.853 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.478 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2027 10 %RANDOM
Rwork0.228 ---
obs-20339 98.1 %-
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: 44.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.46 Å20 Å2
2--0.93 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 322 30 79 3305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.050.0213299
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.192.1124524
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3475370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2080.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022309
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3020.21374
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3370.219
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.380.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8841.51860
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.33522996
X-RAY DIFFRACTIONr_scbond_it4.46831439
X-RAY DIFFRACTIONr_scangle_it6.2534.51528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 166
Rwork0.254 1276
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)
10.35880.12030.2540.78460.40181.90110.06470.03360.0059-0.0206-0.11880.01380.07050.21420.05410.38980.0179-0.01220.383-0.00920.309616.343816.53756.0781
22.8093-1.204-0.88282.94840.46886.05810.07880.0137-0.35780.3055-0.32910.68590.2718-0.28460.25030.3131-0.12810.1040.3429-0.12940.4542-4.9616.135723.6401
32.9279-0.98322.77032.99520.3584.0367-0.4652-0.07780.6493-0.1231-0.1596-0.0863-0.3962-0.14950.62480.37950.0245-0.16880.2717-0.04150.48880.488935.4704-3.2889
46.98151.2328-1.83018.48530.11663.77571.0479-0.34720.61241.3248-0.68340.9378-0.17380.2586-0.36450.6301-0.29220.28050.2298-0.26370.31427.275641.070932.8688
51.4275-0.6439-0.43372.1999-0.34480.56820.0301-0.00490.4890.0384-0.07550.5017-0.14630.14030.04540.4032-0.07840.01730.3192-0.07110.51194.568536.778917.2676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC26 - 372 - 13
2X-RAY DIFFRACTION1AC99 - 22475 - 200
3X-RAY DIFFRACTION2AC38 - 9814 - 74
4X-RAY DIFFRACTION3AC225 - 287201 - 263
5X-RAY DIFFRACTION4AC298 - 414274 - 390
6X-RAY DIFFRACTION5TA839 - 8471 - 9
7X-RAY DIFFRACTION5PB867 - 8731 - 7
8X-RAY DIFFRACTION5AF8751
9X-RAY DIFFRACTION5AE - D871 - 8721

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