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- PDB-3au6: DNA polymerase X from Thermus thermophilus HB8 ternary complex wi... -

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Basic information

Entry
Database: PDB / ID: 3au6
TitleDNA polymerase X from Thermus thermophilus HB8 ternary complex with primer/template DNA and ddGTP
Components
  • 5'-D(*CP*AP*GP*TP*AP*TP*(DDG))-3'
  • 5'-D(*CP*GP*GP*CP*CP*AP*TP*AP*CP*TP*G)-3'
  • DNA polymerase beta family (X family)
KeywordsTRANSFERASE/DNA / RSGI / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / POLXc domain / PHP domain / DNA polymerase / dRP lyase / AP endonuclease / DNA repair / DNA binding / nucleotide binding / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA-(apurinic or apyrimidinic site) lyase / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
: / DNA polymerase/3'-5' exonuclease PolX-like / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / RuvA domain 2-like / Helix-hairpin-helix domain / Beta Polymerase; domain 3 ...: / DNA polymerase/3'-5' exonuclease PolX-like / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / RuvA domain 2-like / Helix-hairpin-helix domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / Metal-dependent hydrolases / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsNakane, S. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA.
Authors: Nakane, S. / Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionJan 28, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Mar 13, 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_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_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.pdbx_leaving_atom_flag / _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_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_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
A: DNA polymerase beta family (X family)
P: 5'-D(*CP*AP*GP*TP*AP*TP*(DDG))-3'
T: 5'-D(*CP*GP*GP*CP*CP*AP*TP*AP*CP*TP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,50312
Polymers69,6603
Non-polymers8439
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.166, 80.166, 268.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta family (X family)


Mass: 64204.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: PolX, TTHA1150 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q5SJ64, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules PT

#2: DNA chain 5'-D(*CP*AP*GP*TP*AP*TP*(DDG))-3'


Mass: 2121.436 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*GP*GP*CP*CP*AP*TP*AP*CP*TP*G)-3'


Mass: 3334.186 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 6 types, 35 molecules

#4: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-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.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.1 Å3/Da / Density % sol: 60.28 % / Mosaicity: 0.272 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50mM Tris-HCl (pH 8.5), 25mM MgSO4 7H2O, 1.8M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2009
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→76.82 Å / Num. obs: 13997 / % possible obs: 99.3 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.065 / Χ2: 0.987 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.427.70.213260.843198.1
3.42-3.559.80.16313850.874199.8
3.55-3.72110.14313491.016199.8
3.72-3.9111.50.12713781199.8
3.91-4.16120.11713740.995199.7
4.16-4.4812.50.11113951.005199.8
4.48-4.9312.80.09713861.029199.5
4.93-5.6412.60.06914191.016199.6
5.64-7.112.60.04114500.992199.5
7.1-5011.90.02715351.009197.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.48 Å32.13 Å
Translation3.48 Å32.13 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0110refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.869 / WRfactor Rfree: 0.326 / WRfactor Rwork: 0.251 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 35.643 / SU ML: 0.601 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.651 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.3194 685 4.9 %RANDOM
Rwork0.2557 ---
obs0.2589 13885 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 129.12 Å2 / Biso mean: 83.2971 Å2 / Biso min: 12.54 Å2
Baniso -1Baniso -2Baniso -3
1-3.96 Å20 Å20 Å2
2--3.96 Å20 Å2
3----7.93 Å2
Refinement stepCycle: LAST / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4425 346 42 26 4839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224935
X-RAY DIFFRACTIONr_bond_other_d0.0020.023371
X-RAY DIFFRACTIONr_angle_refined_deg1.6312.0876745
X-RAY DIFFRACTIONr_angle_other_deg0.94438178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4525559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65422.967209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.93615798
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2661548
X-RAY DIFFRACTIONr_chiral_restr0.0750.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215205
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02964
X-RAY DIFFRACTIONr_mcbond_it0.5311.52791
X-RAY DIFFRACTIONr_mcbond_other0.0621.51139
X-RAY DIFFRACTIONr_mcangle_it0.99724460
X-RAY DIFFRACTIONr_scbond_it1.06732144
X-RAY DIFFRACTIONr_scangle_it1.8764.52285
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.295-3.3810.377510.31791499996.597
3.381-3.4730.451440.319949100199.201
3.473-3.5740.36620.30486693699.145
3.574-3.6830.361460.3189394599.365
3.683-3.8040.347460.3285891299.123
3.804-3.9370.463360.28180885398.945
3.937-4.0850.274340.24481785699.416
4.085-4.2510.361390.23277782499.029
4.251-4.440.274430.22673578199.616
4.44-4.6560.275390.22670875299.335
4.656-4.9070.259440.23767472798.762
4.907-5.2030.347250.28466069099.275
5.203-5.560.33310.2760564398.911
5.56-6.0030.363350.2857861799.352
6.003-6.5720.47290.279540569100
6.572-7.3410.364180.25650052399.044
7.341-8.4640.258220.20544146499.784
8.464-10.3350.233190.18538740899.51
10.335-14.4850.297130.18631533099.394
14.485-76.8170.11790.3217521485.981

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