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- PDB-3po4: Structure of a mutant of the large fragment of DNA polymerase I f... -

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Basic information

Entry
Database: PDB / ID: 3po4
TitleStructure of a mutant of the large fragment of DNA polymerase I from Thermus aquaticus in complex with a blunt-ended DNA and ddATP
Components
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3')
  • DNA (5'-D(*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA polymerase I
KeywordsTRANSFERASE/DNA / DNA polymerase / blunt-ended DNA / processing an A-overhang / DNA primer/template duplex / ddATP / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 ...Taq polymerase, thermostable, exonuclease region / Taq polymerase, exonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / DNA polymerase 1 / Alpha-Beta Plaits - #370 / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / PIN-like domain superfamily / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-dideoxyadenosine triphosphate / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMarx, A. / Diederichs, K. / Obeid, S.
CitationJournal: Chembiochem / Year: 2011
Title: Learning from Directed Evolution: Thermus aquaticus DNA Polymerase Mutants with Translesion Synthesis Activity.
Authors: Obeid, S. / Schnur, A. / Gloeckner, C. / Blatter, N. / Welte, W. / Diederichs, K. / Marx, A.
History
DepositionNov 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ref_seq_dif / 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_asym_id / _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_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_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_ref_seq_dif.details / _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 I
B: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(2DA))-3')
C: DNA (5'-D(*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9269
Polymers68,2633
Non-polymers6636
Water9,872548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-45 kcal/mol
Surface area24820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.525, 113.525, 91.238
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase I / Taq polymerase 1


Mass: 60950.973 Da / Num. of mol.: 1 / Fragment: KLENOW FRAGMENT / Mutation: I614K, M747K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: pol1, polA, polI / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3641.395 Da / Num. of mol.: 1 / Fragment: DNA primer / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 3670.377 Da / Num. of mol.: 1 / Fragment: DNA template / Source method: obtained synthetically

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Non-polymers , 5 types, 554 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-DDS / 2',3'-dideoxyadenosine triphosphate


Mass: 475.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O11P3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M sodium cacodylate, 0.2M KCl, 0.1M Mg(OAc)2, 20% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2KCl11
3Mg(OAc)211
4PEG 800011
5sodium cacodylate12
6KCl12
7Mg(OAc)212
8PEG 800012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 23, 2009
Details: Dynamically bendable mirror, LN2 cooled fixed-exit, Si(111) monochromator
RadiationMonochromator: LN2 cooled fixed-exit, Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 63101 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.96 % / Biso Wilson estimate: 42.02 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.88
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 10.08 % / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.63 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_572)model building
PHENIX(phenix.refine: dev_572)refinement
XDSdata reduction
XDSdata scaling
PHENIXdev_572phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LWM

3lwm


Resolution: 1.8→48.2 Å / SU ML: 0.24 / Isotropic thermal model: isotopic and tls / σ(F): 2.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 3133 4.97 %
Rwork0.164 --
obs0.166 63101 100 %
all-63101 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.38 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.6916 Å2-0 Å2-0 Å2
2--4.6916 Å2-0 Å2
3----0.4333 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 485 39 548 5352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075006
X-RAY DIFFRACTIONf_angle_d1.0886906
X-RAY DIFFRACTIONf_dihedral_angle_d17.3991970
X-RAY DIFFRACTIONf_chiral_restr0.062742
X-RAY DIFFRACTIONf_plane_restr0.005811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82810.25011400.23392672X-RAY DIFFRACTION100
1.8281-1.85810.2571520.20832694X-RAY DIFFRACTION100
1.8581-1.89010.26071400.2032729X-RAY DIFFRACTION100
1.8901-1.92450.24871390.1862681X-RAY DIFFRACTION100
1.9245-1.96150.24271560.19292677X-RAY DIFFRACTION100
1.9615-2.00160.26141410.1832702X-RAY DIFFRACTION100
2.0016-2.04510.19921200.17952733X-RAY DIFFRACTION100
2.0451-2.09270.2391280.17242725X-RAY DIFFRACTION100
2.0927-2.1450.20411550.16782696X-RAY DIFFRACTION100
2.145-2.2030.221360.15782687X-RAY DIFFRACTION100
2.203-2.26780.18651210.16092737X-RAY DIFFRACTION100
2.2678-2.3410.2131370.15912717X-RAY DIFFRACTION100
2.341-2.42470.18531240.16572740X-RAY DIFFRACTION100
2.4247-2.52180.21851290.15922739X-RAY DIFFRACTION100
2.5218-2.63650.21121590.1752703X-RAY DIFFRACTION100
2.6365-2.77550.2161560.17512703X-RAY DIFFRACTION100
2.7755-2.94940.22191310.18122739X-RAY DIFFRACTION100
2.9494-3.17710.19571450.18122752X-RAY DIFFRACTION100
3.1771-3.49670.19811460.17192741X-RAY DIFFRACTION100
3.4967-4.00250.17231630.15352745X-RAY DIFFRACTION100
4.0025-5.04180.13751510.1242777X-RAY DIFFRACTION100
5.0418-48.21370.19581640.17072879X-RAY DIFFRACTION100
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)
11.2664-0.15730.08490.86820.0460.68160.08240.0598-0.2851-0.2284-0.1756-0.12220.34360.11710.05070.29840.06640.06050.190.04690.272341.7193-44.3751-18.4385
20.50890.07360.22530.877-0.16161.3653-0.0135-0.03580.18350.1075-0.0803-0.0653-0.271-0.04310.06520.2236-0.01370.00880.19270.02420.256431.7889-15.0293-2.834
33.55240.5364-0.16480.38980.36740.68460.0369-0.2339-0.16090.19540.1751-0.0577-1.052-0.4394-0.16610.54060.21230.06980.4839-0.0230.24859.6305-13.0982-5.259
41.6471-0.1447-1.26341.7747-0.54141.22470.1196-0.05760.03340.295-0.06160.0982-0.13620.1487-0.05250.34590.08-0.00170.6366-0.07790.29529.0121-19.43844.4694
51.26360.0848-0.12570.6635-0.29691.44040.00080.1091-0.0116-0.1529-0.01370.00780.125-0.21890.00440.195-0.01180.00310.21860.02540.180821.4677-28.9782-15.6872
60.65060.42910.35371.3086-0.080.48840.01180.0966-0.0450.2851-0.0661-0.1284-0.15140.0696-0.00580.19150.0114-0.04230.26010.03530.251238.7643-25.31634.029
70.60530.12860.1290.3920.22380.3104-0.10150.1081-0.07370.09910.104-0.16990.09740.0844-0.00480.18160.0178-0.06920.23950.03510.241640.0945-26.2975.4174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 295:446)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 447:644)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 645:671)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 672:701)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 702:832)
6X-RAY DIFFRACTION6(CHAIN B)
7X-RAY DIFFRACTION7(CHAIN C)

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