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- PDB-7rss: Kod-RI incorporating DNA, n+2 -

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Basic information

Entry
Database: PDB / ID: 7rss
TitleKod-RI incorporating DNA, n+2
Components
  • DNA polymerase
  • Primer
  • Template
KeywordsTRANSFERASE/DNA / Polymerase / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
DNA Polymerase; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / : / 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; Chain A, domain 1 / DNA Polymerase, chain B, domain 1 / : / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsHajjar, M. / Chim, N. / Chaput, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Crystallographic analysis of engineered polymerases synthesizing phosphonomethylthreosyl nucleic acid.
Authors: Hajjar, M. / Chim, N. / Liu, C. / Herdewijn, P. / Chaput, J.C.
History
DepositionAug 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 5, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,0143
Polymers99,0143
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-24 kcal/mol
Surface area37080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.259, 112.000, 149.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein DNA polymerase / Kod-RI


Mass: 90130.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWU9, DNA-directed DNA polymerase
#2: DNA chain Template


Mass: 4898.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Primer


Mass: 3985.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate, sodium citrate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.71→57.03 Å / Num. obs: 30746 / % possible obs: 99.36 % / Redundancy: 2 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.02637 / Rpim(I) all: 0.02637 / Rrim(I) all: 0.03729 / Net I/σ(I): 13.14
Reflection shellResolution: 2.71→2.807 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1368 / Num. unique obs: 3037 / CC1/2: 0.949 / CC star: 0.987 / Rpim(I) all: 0.1368 / Rrim(I) all: 0.1934 / Net I/σ(I) obs: 4.74 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.13_2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VU9

5vu9


Resolution: 2.71→62.087 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 2000 6.51 %
Rwork0.1594 28732 -
obs0.1636 30732 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.09 Å2 / Biso mean: 52.3407 Å2 / Biso min: 19.29 Å2
Refinement stepCycle: final / Resolution: 2.71→62.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6214 573 0 85 6872
Biso mean---42.42 -
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087007
X-RAY DIFFRACTIONf_angle_d0.9389571
X-RAY DIFFRACTIONf_dihedral_angle_d9.6315734
X-RAY DIFFRACTIONf_chiral_restr0.0531028
X-RAY DIFFRACTIONf_plane_restr0.0061128
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.71-2.77780.2491410.18492033100
2.7778-2.85290.26891400.18692011100
2.8529-2.93680.28821400.18452018100
2.9368-3.03160.26781430.1926203799
3.0316-3.140.26611400.19182022100
3.14-3.26570.25221420.17492030100
3.2657-3.41430.24211400.1793202599
3.4143-3.59430.25881420.16972032100
3.5943-3.81950.23641430.16382053100
3.8195-4.11430.22011430.1472058100
4.1143-4.52820.18111420.1323204999
4.5282-5.18320.18571430.126205398
5.1832-6.52910.19781470.16172122100
6.5291-62.0870.21271540.1565218998
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)
13.125-1.2556-0.70242.23480.20290.92680.04690.0885-0.17410.0376-0.01050.46530.0264-0.1183-0.02460.2323-0.05430.01150.22270.02550.336272.901126.4452184.913
22.1407-0.5997-0.67465.46050.36752.9780.15910.3353-0.114-0.3937-0.01930.0772-0.0559-0.0574-0.1720.20820.0134-0.07890.3231-0.01320.217989.0164122.1303173.2898
30.47540.4149-0.07591.7296-0.30990.71950.06220.06590.1018-0.05480.0160.0962-0.14920.0398-0.07470.26170.00580.05830.2675-0.03120.262582.8404152.9248175.4492
41.33620.5424-0.30183.88090.64732.0945-0.22960.1345-0.327-0.54950.2125-0.47270.2560.27510.01020.50180.06720.0850.4226-0.02730.356898.2837143.954153.58
51.1907-0.6923-0.66651.88482.00666.80190.01890.3439-0.1863-0.48330.1830.77190.5768-0.219-0.24290.74440.0278-0.08760.47150.03670.413881.1643145.0346149.2596
63.4861-0.9761-1.63390.877-1.26865.81680.07431.0222-0.3598-1.19290.52970.4016-0.9151-0.4153-0.4921.07440.0086-0.06870.6734-0.04310.422283.5047145.1699146.3692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 225 )A1 - 225
2X-RAY DIFFRACTION2chain 'A' and (resid 226 through 304 )A226 - 304
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 552 )A305 - 552
4X-RAY DIFFRACTION4chain 'A' and (resid 553 through 756 )A553 - 756
5X-RAY DIFFRACTION5chain 'T' and (resid 2 through 16 )T2 - 16
6X-RAY DIFFRACTION6chain 'P' and (resid 1 through 13 )P1 - 13

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