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- PDB-4k8z: KOD Polymerase in binary complex with dsDNA -

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Basic information

Entry
Database: PDB / ID: 4k8z
TitleKOD Polymerase in binary complex with dsDNA
Components
  • DNA (5'-D(*AP*AP*AP*TP*TP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(2DA))-3')
  • DNA polymerase
KeywordsTRANSFERASE/DNA / DNA Polymerase / TRANSFERASE-DNA complex
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 / Intein C-terminal splicing region ...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 / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Homing endonuclease, LAGLIDADG / 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 / Hint domain superfamily / Homing endonuclease / 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
COBALT HEXAMMINE(III) / DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsBergen, K. / Betz, K. / Welte, W. / Diederichs, K. / Marx, A.
CitationJournal: Chembiochem / Year: 2013
Title: Structures of KOD and 9N DNA Polymerases Complexed with Primer Template Duplex
Authors: Bergen, K. / Betz, K. / Welte, W. / Diederichs, K. / Marx, A.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _software.classification
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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
T: DNA (5'-D(*AP*AP*AP*TP*TP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3')
P: DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(2DA))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9257
Polymers98,6153
Non-polymers3104
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-20 kcal/mol
Surface area36330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.870, 111.780, 67.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase /


Mass: 90060.461 Da / Num. of mol.: 1 / Mutation: D141A, E143A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: pol, pol TK0001, TK0001 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P77933, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

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


Mass: 4898.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Primer
#3: DNA chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(2DA))-3')


Mass: 3656.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Template

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Non-polymers , 4 types, 371 molecules

#4: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM Na-Cacodylate, 20mM MgCl2, 1mM Cobalt(III)-hexamminechloride, 1mM Spermine, 20%v/v 2-propanol, , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2012
Details: LN2 cooled fixed-exit Si(111) monochromator Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.29→49.324 Å / Num. all: 49885 / Num. obs: 49755 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.81 / Redundancy: 16.15 % / Biso Wilson estimate: 43.91 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.131 / Net I/σ(I): 16.65
Reflection shellResolution: 2.29→2.35 Å / Redundancy: 13.16 % / Rmerge(I) obs: 1.888 / Mean I/σ(I) obs: 1.81 / Num. unique all: 3506 / Rsym value: 1.965 / % possible all: 96.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
PHENIX(phenix.refine: dev_1243)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WNS
Resolution: 2.29→45.05 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.838 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 2516 5.06 %random
Rwork0.1807 ---
all0.1827 49755 --
obs0.1827 49743 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.07 Å2 / Biso mean: 46.8922 Å2 / Biso min: 20.67 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.29→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6209 529 16 367 7121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036975
X-RAY DIFFRACTIONf_angle_d0.729520
X-RAY DIFFRACTIONf_dihedral_angle_d15.2542703
X-RAY DIFFRACTIONf_chiral_restr0.0511019
X-RAY DIFFRACTIONf_plane_restr0.0031129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2895-2.33350.36231350.3126248296
2.3335-2.38120.33361350.26182574100
2.3812-2.43290.26921320.22992607100
2.4329-2.48950.24461340.22032601100
2.4895-2.55180.26591490.21442561100
2.5518-2.62080.26231200.20742619100
2.6208-2.69790.26621440.20952610100
2.6979-2.7850.2571500.20782607100
2.785-2.88450.25291380.20282575100
2.8845-2.99990.2391320.2032630100
2.9999-3.13640.23281270.20422628100
3.1364-3.30180.25061490.19822616100
3.3018-3.50860.27471450.18652622100
3.5086-3.77930.22711440.1752639100
3.7793-4.15940.17921300.15822671100
4.1594-4.76070.17421530.1392652100
4.7607-5.99580.1941510.16052691100
5.9958-45.05890.16961480.16112842100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.3080.3547-0.3812.56410.94862.9648-0.20710.2456-0.0508-0.5490.1192-0.3131-0.0962-0.01290.08850.3257-0.04170.03510.23640.04420.257182.603433.9534-1.6092
22.8674-0.7566-1.18514.00691.06182.86580.08760.06480.0434-0.2638-0.13240.1097-0.2929-0.26140.04440.24810.0374-0.04840.22630.00770.1672171.616349.567123.9651
30.54680.22610.11661.4185-0.3985-0.017-0.0066-0.0316-0.1320.01390.0045-0.10530.1046-0.0321-0.00620.28070.02430.05350.254-0.00410.2775170.926815.457115.2712
41.3779-0.8886-0.03583.7472-0.18271.0882-0.1147-0.33710.1320.34240.10030.2017-0.1712-0.07490.0070.2376-0.00840.00110.3653-0.06850.348148.761922.169931.826
57.9458-3.2151-0.4752.92740.91862.8478-0.21840.338-0.2042-0.47860.02060.5609-0.1466-0.39840.14750.3534-0.0414-0.04210.2729-0.07360.5137145.269122.903415.0004
67.3534-0.1354-1.64651.1833-0.73643.7205-0.06260.9853-0.8696-0.45910.20380.5836-0.1128-0.3518-0.1720.37860.0552-0.07030.3511-0.10030.6634141.238422.928516.3368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:156)A1 - 156
2X-RAY DIFFRACTION2chain 'A' and (resseq 157:304)A157 - 304
3X-RAY DIFFRACTION3chain 'A' and (resseq 305:532)A305 - 532
4X-RAY DIFFRACTION4chain 'A' and (resseq 533:756)A533 - 756
5X-RAY DIFFRACTION5chain 'T' and (resseq 3:16)T3 - 16
6X-RAY DIFFRACTION6chain 'P' and (resseq 1:11)P1 - 11

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