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- PDB-7tqw: Kod RSGA incorporating PMT, n+2 -

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Basic information

Entry
Database: PDB / ID: 7tqw
TitleKod RSGA incorporating PMT, 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
B family DNA polymerase, thumb 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 / Topoisomerase I; Chain A, domain 4 ...B family DNA polymerase, thumb 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 / Topoisomerase I; Chain A, domain 4 / 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 / Orthogonal Bundle / Mainly Alpha / 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: 3.01 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
DepositionJan 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)98,9753
Polymers98,9753
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-25 kcal/mol
Surface area36030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.136, 111.522, 144.268
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


Mass: 90091.430 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)
Has ligand of interestY
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8K, MOPS, magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.216→64.48 Å / Num. obs: 47878 / % possible obs: 85.13 % / Redundancy: 1.8 % / Biso Wilson estimate: 54.99 Å2 / CC1/2: 0.956 / CC star: 0.989 / Rmerge(I) obs: 0.2462 / Rpim(I) all: 0.2462 / Rrim(I) all: 0.3482 / Net I/σ(I): 2.52
Reflection shellResolution: 2.216→2.296 Å / Redundancy: 1.7 % / Rmerge(I) obs: 2.354 / Num. unique obs: 4637 / CC1/2: 0.362 / CC star: 0.729 / Rpim(I) all: 2.354 / Rrim(I) all: 3.329 / % possible all: 48.68

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RSR

7rsr


Resolution: 3.01→44.036 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2706 1951 10.01 %
Rwork0.1764 17541 -
obs0.1856 19492 92.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.65 Å2 / Biso mean: 54.2403 Å2 / Biso min: 19.73 Å2
Refinement stepCycle: final / Resolution: 3.01→44.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6204 573 0 0 6777
Num. residues----784
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.01-3.08530.37381400.2627126395
3.0853-3.16870.33961400.2374125695
3.1687-3.26190.32041390.2305124694
3.2619-3.36710.33631420.211128194
3.3671-3.48740.32741390.201124493
3.4874-3.6270.28611370.2078122892
3.627-3.7920.30231410.1813127993
3.792-3.99180.26961390.1615124993
3.9918-4.24170.24611390.1489125193
4.2417-4.56890.21931410.1362125892
4.5689-5.02810.24651360.1451123191
5.0281-5.75430.25911380.16123689
5.7543-7.24460.25071390.1806125489
7.2446-44.0360.22951410.1661126586
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)
10.14620.0310.09960.20610.0128-0.1452-0.06120.0254-0.07250.0614-0.02150.1428-0.08860.0926-00.23110.02380.01180.29650.00680.383356.4674134.8158182.6921
20.4466-0.0062-0.17160.5379-0.30840.03060.08260.01790.1061-0.3976-0.0321-0.31620.0492-0.07460.00010.3030.04310.04070.2931-0.01470.287984.9539117.6961175.1796
30.2289-0.13730.30310.4750.13790.36260.10080.04720.077-0.2992-0.0402-0.1823-0.033-0.047900.350.00830.06620.32820.0420.313587.4544121.7929169.0404
40.42890.2070.33950.4038-0.31270.05570.045-0.0588-0.0602-0.10620.0480.0087-0.0368-0.0102-00.2780.01170.06780.3211-0.01630.281278.7251156.1702168.8139
50.7376-0.2499-0.21790.7578-0.53480.75650.0353-0.0086-0.0581-0.0671-0.0007-0.18120.13290.068300.36610.00570.08290.3495-0.0290.236496.504143.3102148.4251
60.19120.1995-0.15240.1879-0.11270.06750.30110.26620.0858-0.06220.2320.5268-0.11690.17970.10010.44830.0928-0.02770.453-0.07910.346879.6098144.6537143.8253
70.08880.02870.06680.00550.01660.03310.35460.4884-0.07150.00710.0253-0.2077-0.41320.1368-0.00050.68410.14340.00320.73920.08050.494680.9858143.5227137.816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 110 )A1 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 214 )A111 - 214
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 337 )A215 - 337
4X-RAY DIFFRACTION4chain 'A' and (resid 338 through 552 )A338 - 552
5X-RAY DIFFRACTION5chain 'A' and (resid 553 through 756 )A553 - 756
6X-RAY DIFFRACTION6chain 'T' and (resid 2 through 16 )T2 - 16
7X-RAY DIFFRACTION7chain 'P' and (resid 1 through 11 )P1 - 11

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