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

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Basic information

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


DNA-templated DNA replication / 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-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. ...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-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Helix Hairpins / 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. 9oN-7 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 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 1.1Sep 12, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set
Item: _pdbx_related_exp_data_set.data_reference / _pdbx_related_exp_data_set.metadata_reference
Revision 1.2Jan 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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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)99,36110
Polymers98,3743
Non-polymers9877
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-42 kcal/mol
Surface area35540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.688, 94.964, 158.735
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. 9oN-7 (archaea) / 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, 186 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#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.: 179 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging 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: 0.999973488495 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999973488495 Å / Relative weight: 1
ReflectionResolution: 2→47.482 Å / Num. obs: 130652 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rrim(I) all: 0.142 / Net I/σ(I): 7.88
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 0.37 / Num. unique obs: 21057 / Rrim(I) all: 3.603 / % possible all: 99.6

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Processing

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

4k8x


Resolution: 2.003→47.482 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 30.83
RfactorNum. reflection% reflection
Rfree0.2332 6604 5.06 %
Rwork0.1894 --
obs0.1916 130623 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.003→47.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6208 548 53 179 6988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087033
X-RAY DIFFRACTIONf_angle_d0.9249602
X-RAY DIFFRACTIONf_dihedral_angle_d13.4334162
X-RAY DIFFRACTIONf_chiral_restr0.0531025
X-RAY DIFFRACTIONf_plane_restr0.0051146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0028-2.02560.49452380.45294113X-RAY DIFFRACTION99
2.0256-2.04940.42692330.43164069X-RAY DIFFRACTION100
2.0494-2.07440.41132150.41144211X-RAY DIFFRACTION100
2.0744-2.10070.41811890.38694117X-RAY DIFFRACTION100
2.1007-2.12830.3762080.37164149X-RAY DIFFRACTION100
2.1283-2.15750.4081990.36914170X-RAY DIFFRACTION100
2.1575-2.18830.3872100.34974144X-RAY DIFFRACTION100
2.1883-2.2210.40731880.33434136X-RAY DIFFRACTION100
2.221-2.25570.32412270.32684136X-RAY DIFFRACTION99
2.2557-2.29270.36422260.31764123X-RAY DIFFRACTION99
2.2927-2.33220.34992210.30014126X-RAY DIFFRACTION99
2.3322-2.37460.3022010.2864189X-RAY DIFFRACTION100
2.3746-2.42030.30381960.27074112X-RAY DIFFRACTION100
2.4203-2.46970.31842230.26174127X-RAY DIFFRACTION100
2.4697-2.52340.30452060.24564171X-RAY DIFFRACTION100
2.5234-2.58210.30442540.23114082X-RAY DIFFRACTION100
2.5821-2.64660.30962310.22814140X-RAY DIFFRACTION100
2.6466-2.71820.25152440.22784084X-RAY DIFFRACTION100
2.7182-2.79820.27122540.21924107X-RAY DIFFRACTION100
2.7982-2.88850.29672140.21924200X-RAY DIFFRACTION100
2.8885-2.99170.2682400.19424093X-RAY DIFFRACTION100
2.9917-3.11140.24732080.19894117X-RAY DIFFRACTION100
3.1114-3.2530.25222250.17854152X-RAY DIFFRACTION100
3.253-3.42450.18762030.16884154X-RAY DIFFRACTION100
3.4245-3.6390.21922440.16984151X-RAY DIFFRACTION100
3.639-3.91980.21372240.15344127X-RAY DIFFRACTION100
3.9198-4.3140.13772290.12424128X-RAY DIFFRACTION100
4.314-4.93770.14352250.11384106X-RAY DIFFRACTION100
4.9377-6.21880.20752110.13654140X-RAY DIFFRACTION100
6.2188-47.49530.17652180.13494145X-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)
11.49450.81340.89591.45850.64981.7854-0.02730.07-0.1314-0.02150.0169-0.28290.1040.2189-0.01860.27340.03550.03640.38340.05810.3359109.829996.90933.4624
22.75051.45850.09242.04660.31471.1108-0.0075-0.23080.33660.0674-0.13270.0115-0.20550.12990.14390.37450.0057-0.07940.48760.06730.3986109.7231108.231117.5322
31.3253-0.1897-0.7870.67430.42122.8903-0.1076-0.0294-0.20520.1287-0.03220.05220.2803-0.18190.15070.378-0.05670.00120.34740.07370.34678.821994.46623.9556
42.81640.367-0.05242.9036-0.84313.8168-0.0272-0.28630.41570.1890.089-0.3344-0.44450.2259-0.0640.31880.0087-0.04720.4088-0.06830.454187.4639126.978429.4918
50.4991-0.35140.81672.4995-1.24311.69360.07060.18350.1249-0.1727-0.0728-0.3896-0.2358-0.1962-0.12210.38640.00420.02540.43550.07360.407779.7406118.392214.7602
62.0449-2.45240.66193.0083-1.21481.62080.13720.37640.0802-0.13-0.21610.0809-0.297-0.02320.09270.4510.0179-0.03690.46510.02980.374277.4113121.011817.081
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 363 )
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 588 )
4X-RAY DIFFRACTION4chain 'A' and (resid 589 through 758 )
5X-RAY DIFFRACTION5chain 'T' and (resid 2 through 16 )
6X-RAY DIFFRACTION6chain 'P' and (resid 1 through 12 )

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