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- PDB-3sv4: Crystal structure of the large fragment of DNA polymerase I from ... -

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Basic information

Entry
Database: PDB / ID: 3sv4
TitleCrystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in an open binary complex with dT as templating nucleobase
Components
  • (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
  • DNA polymerase I, thermostable
KeywordsTRANSFERASE/DNA / DNA polymerase / TRANSFERASE-DNA complex
Function / homology
Function and homology information


nucleoside binding / 5'-3' exonuclease activity / DNA-templated DNA replication / double-strand break repair / 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 / DNA polymerase 1 / 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 / DNA polymerase 1 / Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / 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
FORMIC ACID / DNA / DNA (> 10) / DNA polymerase I, thermostable
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.99 Å
AuthorsBetz, K. / Diederichs, K. / Marx, A.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.
Authors: Betz, K. / Malyshev, D.A. / Lavergne, T. / Welte, W. / Diederichs, K. / Dwyer, T.J. / Ordoukhanian, P. / Romesberg, F.E. / Marx, A.
History
DepositionJul 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Sep 12, 2012Group: Database references
Revision 1.3Sep 13, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_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, thermostable
B: (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC))-3')
C: (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,98115
Polymers69,4943
Non-polymers48712
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-28 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.388, 108.388, 90.467
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, thermostable / Taq polymerase 1


Mass: 60936.965 Da / Num. of mol.: 1 / Fragment: Klenow Fragment, UNP residues 293-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: pol I, pol1, polA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P19821, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules BC

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


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesizer
#3: DNA chain (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')


Mass: 4939.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesizer

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Non-polymers , 3 types, 332 molecules

#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.21 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18% PEG 8000, 0.2M MgFormate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.99→47.1 Å / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.98 % / Net I/σ(I): 13.79
Reflection shellResolution: 1.99→2.12 Å / Mean I/σ(I) obs: 2.06 / Num. unique all: 6685 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.7.1_743phasing
RefinementStarting model: PDB ENTRY 4KTQ

4ktq


Resolution: 1.99→46.933 Å / SU ML: 0.56 / Isotropic thermal model: isotropic and tls / σ(F): 1.3 / Phase error: 20.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 4049 5.02 %random
Rwork0.1788 ---
obs0.1807 80646 99.54 %-
all-81018 --
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.147 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1315 Å20 Å2-0 Å2
2--1.1315 Å2-0 Å2
3----2.263 Å2
Refinement stepCycle: LAST / Resolution: 1.99→46.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 550 30 320 5123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035040
X-RAY DIFFRACTIONf_angle_d0.776952
X-RAY DIFFRACTIONf_dihedral_angle_d15.8741960
X-RAY DIFFRACTIONf_chiral_restr0.043761
X-RAY DIFFRACTIONf_plane_restr0.003812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9945-2.0180.37981250.31852321X-RAY DIFFRACTION87
2.018-2.04260.24011300.27652673X-RAY DIFFRACTION100
2.0426-2.06840.29931480.24282634X-RAY DIFFRACTION100
2.0684-2.09560.26081360.24012609X-RAY DIFFRACTION100
2.0956-2.12440.26831270.23132681X-RAY DIFFRACTION100
2.1244-2.15470.2731340.22172686X-RAY DIFFRACTION100
2.1547-2.18690.27721340.21832629X-RAY DIFFRACTION100
2.1869-2.2210.25851060.2092672X-RAY DIFFRACTION100
2.221-2.25740.22571450.19852704X-RAY DIFFRACTION100
2.2574-2.29640.21711400.19062633X-RAY DIFFRACTION100
2.2964-2.33810.25651300.19712663X-RAY DIFFRACTION100
2.3381-2.38310.24981130.19952638X-RAY DIFFRACTION100
2.3831-2.43170.26761250.20252708X-RAY DIFFRACTION100
2.4317-2.48460.24581380.19632661X-RAY DIFFRACTION100
2.4846-2.54240.26391560.18752612X-RAY DIFFRACTION100
2.5424-2.6060.24671510.18272691X-RAY DIFFRACTION100
2.606-2.67640.20251410.18822631X-RAY DIFFRACTION100
2.6764-2.75520.24031370.18612643X-RAY DIFFRACTION100
2.7552-2.84410.23021550.18122632X-RAY DIFFRACTION100
2.8441-2.94570.21041530.17482659X-RAY DIFFRACTION100
2.9457-3.06370.22431270.16892667X-RAY DIFFRACTION100
3.0637-3.20310.20221480.17222637X-RAY DIFFRACTION100
3.2031-3.37190.16311380.16032667X-RAY DIFFRACTION100
3.3719-3.58310.19831510.16292622X-RAY DIFFRACTION100
3.5831-3.85960.18391710.15442642X-RAY DIFFRACTION100
3.8596-4.24780.17531680.14352602X-RAY DIFFRACTION100
4.2478-4.86190.19481210.13582689X-RAY DIFFRACTION100
4.8619-6.12330.21641470.17682637X-RAY DIFFRACTION100
6.1233-46.94640.21671540.18852654X-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)
10.52480.42880.18421.90810.41771.06480.0357-0.0715-0.01920.1109-0.0065-0.07980.00720.0794-0.03270.1277-0.02790.00720.22030.0260.15837.655-26.3387-8.5647
21.95340.6463-0.05561.6041-1.1352.47880.0919-0.29870.22730.27210.15450.3641-0.4667-0.5358-0.16190.24380.05150.06710.34090.0170.217814.5802-22.2552-11.7121
34.50081.3478-0.48671.5141-0.60790.51380.14570.1921-0.61580.3825-0.3798-0.0349-0.09330.69230.1890.27540.0635-0.01130.3418-0.00130.252436.5555-22.7344.3165
41.65681.537-1.26323.70730.9223.0019-0.32960.16920.00020.23170.28170.068-0.09440.08030.10120.24440.0531-0.01130.23870.01410.131233.4745-22.68814.0917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 293:603)
2X-RAY DIFFRACTION2chain 'A' and (resseq 604:832)
3X-RAY DIFFRACTION3chain 'B'
4X-RAY DIFFRACTION4chain 'C'

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