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- PDB-5omq: Ternary complex of 9N DNA polymerase in the replicative state wit... -

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Basic information

Entry
Database: PDB / ID: 5omq
TitleTernary complex of 9N DNA polymerase in the replicative state with three metal ions in the active site
Components
  • DNA Primer
  • DNA Template
  • DNA polymerase
KeywordsTRANSFERASE / ternary complex / DNA polymerase / triphosphate
Function / homology
Function and homology information


nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain ...DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Helix Hairpins / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / : / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus sp. (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsBetz, K. / Marx, A. / Diederichs, K.
CitationJournal: PLoS ONE / Year: 2017
Title: Crystal structures of ternary complexes of archaeal B-family DNA polymerases.
Authors: Kropp, H.M. / Betz, K. / Wirth, J. / Diederichs, K. / Marx, A.
History
DepositionAug 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase
T: DNA Template
P: DNA Primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2119
Polymers98,3743
Non-polymers8376
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-47 kcal/mol
Surface area35670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.793, 93.678, 158.205
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase


Mass: 89826.570 Da / Num. of mol.: 1 / Mutation: D141A, E143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus sp. (strain 9oN-7) (archaea)
Strain: 9oN-7 / Gene: pol, polA / Production host: Escherichia coli (E. coli) / References: UniProt: Q56366, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA Template


Mass: 4930.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA Primer


Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 96 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#8: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate trihydrate pH 4.5, 6% isopropanol, 36% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999975 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999975 Å / Relative weight: 1
ReflectionResolution: 2.199→46.839 Å / Num. obs: 97025 / % possible obs: 99.6 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rrim(I) all: 0.108 / Net I/σ(I): 8.62
Reflection shellResolution: 2.199→2.33 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 15527 / CC1/2: 0.476 / Rrim(I) all: 1.549 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.12rc0_2787: ???)refinement
XDSdata reduction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K8X

4k8x


Resolution: 2.199→46.839 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 31.94
RfactorNum. reflection% reflection
Rfree0.2483 4955 5.11 %
Rwork0.193 --
obs0.1959 96987 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.199→46.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6208 527 49 90 6874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087025
X-RAY DIFFRACTIONf_angle_d0.9349592
X-RAY DIFFRACTIONf_dihedral_angle_d14.1654164
X-RAY DIFFRACTIONf_chiral_restr0.0521023
X-RAY DIFFRACTIONf_plane_restr0.0061151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1994-2.22440.4631400.40682943X-RAY DIFFRACTION95
2.2244-2.25060.47131630.46373072X-RAY DIFFRACTION99
2.2506-2.2780.40811640.39923044X-RAY DIFFRACTION100
2.278-2.30690.36611590.34453098X-RAY DIFFRACTION100
2.3069-2.33720.33791550.32683081X-RAY DIFFRACTION100
2.3372-2.36920.35341620.31263082X-RAY DIFFRACTION100
2.3692-2.40310.36851550.30743124X-RAY DIFFRACTION100
2.4031-2.4390.35391710.29613028X-RAY DIFFRACTION100
2.439-2.47710.30691470.29083141X-RAY DIFFRACTION100
2.4771-2.51770.33571570.27943040X-RAY DIFFRACTION100
2.5177-2.56110.30931880.26743042X-RAY DIFFRACTION99
2.5611-2.60770.33922020.2663051X-RAY DIFFRACTION100
2.6077-2.65780.31621510.25243087X-RAY DIFFRACTION100
2.6578-2.71210.31151840.25583026X-RAY DIFFRACTION100
2.7121-2.7710.36441960.24843093X-RAY DIFFRACTION100
2.771-2.83550.30611400.25593090X-RAY DIFFRACTION100
2.8355-2.90640.33131700.24533073X-RAY DIFFRACTION100
2.9064-2.98490.3081850.21633011X-RAY DIFFRACTION100
2.9849-3.07280.25961400.20893123X-RAY DIFFRACTION100
3.0728-3.17190.31461700.21653099X-RAY DIFFRACTION100
3.1719-3.28530.24941740.19913046X-RAY DIFFRACTION100
3.2853-3.41680.27691420.20613078X-RAY DIFFRACTION100
3.4168-3.57220.25471990.19373059X-RAY DIFFRACTION100
3.5722-3.76050.24591660.17513079X-RAY DIFFRACTION100
3.7605-3.99590.25181660.15833067X-RAY DIFFRACTION99
3.9959-4.30430.16111690.13493039X-RAY DIFFRACTION99
4.3043-4.73710.16241590.1263089X-RAY DIFFRACTION100
4.7371-5.42170.17521750.12483067X-RAY DIFFRACTION100
5.4217-6.82730.21361280.15613096X-RAY DIFFRACTION99
6.8273-46.84960.18331780.13663064X-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)
11.42681.14550.82991.55570.67141.79630.0366-0.0368-0.080.0046-0.0801-0.2450.15170.25490.0080.34970.06140.040.68070.05850.4226109.972395.27113.5534
22.63751.9112-0.4832.7563-0.15210.85770.1127-0.33480.24570.2111-0.19790.0269-0.11440.22330.09320.3942-0.0207-0.05810.73430.0580.4227109.7977106.532917.5489
32.0783-0.3937-1.23080.42380.69223.9539-0.06460.0289-0.19020.0879-0.06610.0570.1467-0.20430.16220.3956-0.07010.00440.43340.07250.395379.726293.151221.2165
41.29670.4835-0.18772.823-0.43561.3903-0.0131-0.22530.23480.24170.0343-0.3477-0.21830.1465-0.0080.33130.0168-0.05820.6363-0.04230.416685.4489119.908831.11
50.0072-0.6270.02329.1269-1.69420.46220.12740.21320.1212-0.1851-0.0448-0.0525-0.0645-0.1377-0.10160.3250.024-0.02970.59840.07380.347778.8997117.548215.2602
62.5334-3.14270.88583.777-1.13791.60280.22810.5518-0.0813-0.3061-0.30510.1484-0.1325-0.04140.10870.42740.0119-0.04520.64830.00850.43577.6375119.589416.9496
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 214 )
2X-RAY DIFFRACTION2chain 'A' and (resid 215 through 364 )
3X-RAY DIFFRACTION3chain 'A' and (resid 365 through 552 )
4X-RAY DIFFRACTION4chain 'A' and (resid 553 through 758 )
5X-RAY DIFFRACTION5chain 'T' and (resid 3 through 16 )
6X-RAY DIFFRACTION6chain 'P' and (resid 1 through 12 )

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