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- PDB-5omf: Closed, ternary structure of KOD DNA polymerase -

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Basic information

Entry
Database: PDB / ID: 5omf
TitleClosed, ternary structure of KOD DNA polymerase
Components
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3')
  • DNA (5'-D(P*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
  • DNA polymerase,DNA polymerase,DNA polymerase
KeywordsDNA BINDING PROTEIN / DNA replication DNA polymerase archaea
Function / homology
Function and homology information


intron homing / intein-mediated protein splicing / exonuclease activity / DNA-templated DNA replication / endonuclease activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
DNA polymerase II intein domain IV / DNA polymerase II intein Domain IV / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / Homing endonuclease, LAGLIDADG ...DNA polymerase II intein domain IV / DNA polymerase II intein Domain IV / LAGLIDADG-like domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / Homing endonuclease, LAGLIDADG / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / B family DNA polymerase, finger domain / Palm domain of DNA polymerase / B family DNA polymerase, palm domain / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Homing endonuclease / Hint domain superfamily / 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 / : / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.092 Å
AuthorsKropp, H.M. / Betz, K. / Wirth, J. / Diederichs, K. / Marx, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
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
DepositionJul 31, 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 1.2Feb 20, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn / pdbx_seq_map_depositor_info
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 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_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.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,DNA polymerase,DNA polymerase
T: DNA (5'-D(P*CP*TP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')
P: DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,00914
Polymers99,8593
Non-polymers1,15011
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-30 kcal/mol
Surface area35890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.909, 147.559, 71.142
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-901-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase,DNA polymerase,DNA polymerase


Mass: 90060.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Gene: pol, TK0001 / Production host: Escherichia coli (E. coli)
References: UniProt: P77933, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 2 molecules TP

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


Mass: 4930.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3')


Mass: 4868.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 280 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M DL-glutamatic acid, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine monohydrochloride, 0.2 M DL-serine, 0.1 M Hepes/ 0.1 M Mops, 20 % glycerol, 10 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999766 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999766 Å / Relative weight: 1
ReflectionResolution: 2.09→49.19 Å / Num. obs: 127923 / % possible obs: 98.8 % / Redundancy: 3.56 % / CC1/2: 0.993 / Rrim(I) all: 0.185 / Net I/σ(I): 6.37
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 3.41 % / Mean I/σ(I) obs: 0.81 / Num. unique all: 20049 / CC1/2: 0.285 / Rrim(I) all: 1.72 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2815: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K8Z

4k8z


Resolution: 2.092→46.266 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 26.38
RfactorNum. reflection% reflection
Rfree0.2335 6406 5.01 %
Rwork0.1953 --
obs0.1973 127892 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.092→46.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6209 527 67 269 7072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027005
X-RAY DIFFRACTIONf_angle_d0.5279556
X-RAY DIFFRACTIONf_dihedral_angle_d18.9654158
X-RAY DIFFRACTIONf_chiral_restr0.0421024
X-RAY DIFFRACTIONf_plane_restr0.0031140
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0922-2.1160.35651760.35393316X-RAY DIFFRACTION81
2.116-2.14090.36042240.34254043X-RAY DIFFRACTION100
2.1409-2.1670.37842230.33544091X-RAY DIFFRACTION100
2.167-2.19450.36771930.3324056X-RAY DIFFRACTION99
2.1945-2.22330.35732140.32494112X-RAY DIFFRACTION99
2.2233-2.25380.34411970.31924062X-RAY DIFFRACTION99
2.2538-2.2860.37292290.31684028X-RAY DIFFRACTION99
2.286-2.32010.33092320.29164020X-RAY DIFFRACTION100
2.3201-2.35640.3361990.28164133X-RAY DIFFRACTION100
2.3564-2.3950.33422100.27674113X-RAY DIFFRACTION100
2.395-2.43630.29812320.2664081X-RAY DIFFRACTION100
2.4363-2.48060.30922070.26424085X-RAY DIFFRACTION100
2.4806-2.52830.3112020.2554103X-RAY DIFFRACTION100
2.5283-2.57990.27072290.24924097X-RAY DIFFRACTION100
2.5799-2.6360.26442290.24024119X-RAY DIFFRACTION100
2.636-2.69730.271790.23184072X-RAY DIFFRACTION100
2.6973-2.76470.23892250.22484094X-RAY DIFFRACTION100
2.7647-2.83950.28942150.22114092X-RAY DIFFRACTION100
2.8395-2.9230.24422250.21574062X-RAY DIFFRACTION100
2.923-3.01740.26722390.20794079X-RAY DIFFRACTION100
3.0174-3.12520.2672000.20034065X-RAY DIFFRACTION100
3.1252-3.25030.25112180.18543996X-RAY DIFFRACTION97
3.2503-3.39820.2592270.17194027X-RAY DIFFRACTION99
3.3982-3.57720.20822120.16434119X-RAY DIFFRACTION100
3.5772-3.80130.19621740.15254130X-RAY DIFFRACTION100
3.8013-4.09460.17862520.13954017X-RAY DIFFRACTION99
4.0946-4.50640.17112120.12744093X-RAY DIFFRACTION100
4.5064-5.15770.16492390.13124089X-RAY DIFFRACTION100
5.1577-6.49530.18321980.17133984X-RAY DIFFRACTION97
6.4953-46.27740.18211950.17344108X-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)
11.9147-0.1609-1.11470.49340.33182.10520.0475-0.0550.1658-0.01180.0355-0.0187-0.01060.1128-0.10580.2601-0.0162-0.0390.35220.02140.3283-16.546240.1226-7.0079
24.6329-0.12810.36372.14950.70312.34420.12380.1301-0.5047-0.0653-0.00480.02420.28770.0024-0.09160.28380.0035-0.00010.37520.05310.2964-9.0428.3424-23.6353
31.40320.33310.41280.59370.03650.4912-0.02450.1474-0.0271-0.06530.0340.06240.0395-0.0456-0.00210.21880.0163-0.02030.3029-0.00010.2454-39.839624.9613-16.1486
43.1685-1.41020.81391.8514-0.60831.47910.30530.6337-0.3253-0.4405-0.2591-0.23160.4390.3863-0.04060.45650.08370.0220.4585-0.05950.4547-28.36013.6489-30.2191
52.0739-2.39430.25078.98880.44251.20920.2391-0.029-0.5465-0.2764-0.1716-0.40260.27470.2462-0.03030.30860.03150.01330.31630.04710.5186-30.66980.4494-14.1069
63.4228-2.74461.69384.1695-1.1223.66040.0143-0.2851-0.54680.32180.12930.17870.51220.0785-0.10420.36580.0322-0.00740.33910.03080.4627-30.7319-0.8361-15.5315
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 304 )
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 552 )
4X-RAY DIFFRACTION4chain 'A' and (resid 553 through 756 )
5X-RAY DIFFRACTION5chain 'T' and (resid 4 through 16 )
6X-RAY DIFFRACTION6chain 'P' and (resid 1 through 12 )

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