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- PDB-7rsr: Kod-RI incorporating PMT, n+2 -

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Basic information

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


DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
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 ...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 superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
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: 1.98 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 2.0Sep 28, 2022Group: Database references / Non-polymer description / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _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 / _entity.formula_weight
Revision 2.1Oct 5, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Oct 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
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-23 kcal/mol
Surface area36610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.780, 111.618, 149.026
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 / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.49 %
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: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→45.107 Å / Num. obs: 77125 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 36.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07356 / Rpim(I) all: 0.02978 / Rrim(I) all: 0.07946 / Net I/σ(I): 17.86
Reflection shellResolution: 1.98→2.051 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.204 / Num. unique obs: 7617 / CC1/2: 0.741 / CC star: 0.923 / Rpim(I) all: 0.4792 / Rrim(I) all: 1.298 / % possible all: 99.97

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Processing

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

5vu9


Resolution: 1.98→42.556 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 2000 2.59 %
Rwork0.176 75093 -
obs0.177 77093 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.97 Å2 / Biso mean: 52.8368 Å2 / Biso min: 21.1 Å2
Refinement stepCycle: final / Resolution: 1.98→42.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6214 573 0 243 7030
Biso mean---50.47 -
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077017
X-RAY DIFFRACTIONf_angle_d0.899580
X-RAY DIFFRACTIONf_dihedral_angle_d10.1245721
X-RAY DIFFRACTIONf_chiral_restr0.0561027
X-RAY DIFFRACTIONf_plane_restr0.0061131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.98-2.02950.25421410.25285291
2.0295-2.08440.24311400.23335280
2.0844-2.14570.22711420.21815306
2.1457-2.2150.27921410.2025296
2.215-2.29410.22861410.20395314
2.2941-2.3860.2331420.19185310
2.386-2.49460.21071420.18855330
2.4946-2.62610.22241430.18855354
2.6261-2.79060.2071410.1875332
2.7906-3.0060.22121430.18335367
3.006-3.30840.26351440.18815379
3.3084-3.78680.21491430.16935411
3.7868-4.770.17671460.14725452
4.77-42.5560.18781510.16265671
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)
11.66930.2472-1.07324.1172-1.69372.2477-0.02090.17120.06570.15210.66491.4155-0.1041-0.6494-0.39170.25840.02870.07570.38730.18960.707658.1777135.3923189.479
23.6788-2.3169-0.75983.03210.62981.38040.06020.1655-0.3303-0.0428-0.03360.06340.24910.1458-0.03190.2216-0.0153-0.01370.1784-0.00370.277986.8907117.8215181.1226
32.1072-1.29590.04874.331.00242.18090.16040.3842-0.166-0.352-0.0874-0.01020.0990.0803-0.0780.2140.0231-0.01060.299-0.02080.30589.3676121.8719174.7623
40.88521.0677-0.47382.4225-0.99181.23520.04730.05660.00310.0376-0.00510.0461-0.16410.0346-0.02450.24710.01670.03840.1921-0.01880.249180.4464156.4238174.7143
51.31870.7059-0.09923.88720.4351.7804-0.18660.1007-0.3448-0.64890.2222-0.59580.19240.2795-0.05250.42840.02530.11410.3573-0.01830.338497.769143.4473153.4867
61.7812-0.63030.36831.66562.04946.01820.06950.3791-0.1957-0.5810.12830.59330.40020.0719-0.17670.6459-0.0083-0.10950.3377-0.00280.348880.675144.5248149.3314
73.1968-1.4408-1.86581.7318-1.34916.08620.04541.1015-0.2322-0.92240.35410.6465-0.85-0.2713-0.22991.0293-0.0625-0.15970.6783-0.0410.400382.0316143.3321143.3855
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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