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- PDB-2flp: Binary complex of the catalytic core of human DNA polymerase iota... -

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Basic information

Entry
Database: PDB / ID: 2flp
TitleBinary complex of the catalytic core of human DNA polymerase iota with DNA (template G)
Components
  • DNA polymerase iotaPOLI
  • DNA primer strand
  • DNA template strand
KeywordsREPLICATION/DNA / DNA polymerase / lesion bypass / Y-family / binary complex / template G / REPLICATION-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
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
DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNair, D.T. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
CitationJournal: Structure / Year: 2006
Title: An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site.
Authors: Nair, D.T. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionJan 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: DNA template strand
P: DNA primer strand
A: DNA polymerase iota


Theoretical massNumber of molelcules
Total (without water)52,4753
Polymers52,4753
Non-polymers00
Water2,072115
1
T: DNA template strand
P: DNA primer strand
A: DNA polymerase iota

T: DNA template strand
P: DNA primer strand
A: DNA polymerase iota


Theoretical massNumber of molelcules
Total (without water)104,9506
Polymers104,9506
Non-polymers00
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)98.367, 98.367, 202.497
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: DNA chain DNA template strand


Mass: 3356.182 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA primer strand


Mass: 2091.414 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA polymerase iota / POLI / RAD30 homolog B / Eta2


Mass: 47027.344 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 23107 / Num. obs: 22540 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE ALZ

Resolution: 2.4→36.51 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.888 / SU B: 8.627 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: CNS 1.1 WAS ALSO USED FOR REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.27616 2224 9.9 %RANDOM
Rwork0.22803 ---
obs0.2328 20314 96.22 %-
all-23107 --
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: 45.563 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 322 0 115 3250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.060.0213212
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.1822.1034406
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3125363
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_restr0.2130.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022265
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3010.21457
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.2181
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4070.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5160.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0181.51829
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.3722942
X-RAY DIFFRACTIONr_scbond_it4.23931383
X-RAY DIFFRACTIONr_scangle_it5.8524.51464
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.344 151
Rwork0.252 1408
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)
10.3643-0.0330.17540.60720.38081.83520.01770.01270.0445-0.0502-0.10370.05180.05180.17030.0860.57420.0123-0.02420.52590.00350.466716.653516.57016.0722
24.5064-1.9551-1.34656.12211.84434.09130.17350.1731-0.21540.6094-0.63081.24690.5297-0.37790.45730.5604-0.1560.12080.5295-0.17650.6514-4.53415.799623.9983
33.4874-0.94211.61012.06620.48332.6934-0.39620.06980.7969-0.068-0.222-0.0193-0.0599-0.11830.61820.52660.0238-0.19390.421-0.03190.67460.793135.4412-3.1754
43.59184.1711-0.338711.45521.07943.87061.33070.06710.66722.0038-0.99930.99860.01570.4902-0.33140.9025-0.35720.38220.2743-0.35430.47198.380640.781133.4158
50.6278-0.6838-0.07011.34990.96460.6126-0.07370.01760.92750.0805-0.04230.61270.04240.08360.1160.5529-0.1144-0.01430.4595-0.06040.815.268937.959717.281
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 DIFFRACTION5TA839 - 8473 - 11
7X-RAY DIFFRACTION5PB867 - 8731 - 7

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