[English] 日本語
Yorodumi
- PDB-7rsu: TNA polymerase, n+2 product -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rsu
TitleTNA polymerase, n+2 product
Components
  • DNA polymerase
  • Primer
  • Template
KeywordsTRANSFERASE/DNA / 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: 2.1 Å
AuthorsMaola, V. / Chaput, J. / Chim, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Synthesis and Polymerase Recognition of Threose Nucleic Acid Triphosphates Equipped with Diverse Chemical Functionalities.
Authors: Li, Q. / Maola, V.A. / Chim, N. / Hussain, J. / Lozoya-Colinas, A. / Chaput, J.C.
History
DepositionAug 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)99,4643
Polymers99,4643
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-21 kcal/mol
Surface area35840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.540, 111.694, 148.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein DNA polymerase /


Mass: 89989.391 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: 5525.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Primer


Mass: 3948.546 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.: 287 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M magnesium acetate tetrahydrate, 0.1M 3-(N-morpholino)propanesulfonic acid, 10% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45.295 Å / Num. obs: 64028 / % possible obs: 97.92 % / Redundancy: 6.1 % / Biso Wilson estimate: 34.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07404 / Net I/σ(I): 16.77
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 6036 / CC1/2: 0.844

-
Processing

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

5vu9


Resolution: 2.1→45.295 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 1972 3.12 %
Rwork0.1816 61197 -
obs0.1831 63169 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.13 Å2 / Biso mean: 44.4328 Å2 / Biso min: 17.59 Å2
Refinement stepCycle: final / Resolution: 2.1→45.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6204 552 0 287 7043
Biso mean---46.99 -
Num. residues----783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076959
X-RAY DIFFRACTIONf_angle_d0.9049497
X-RAY DIFFRACTIONf_dihedral_angle_d9.9634108
X-RAY DIFFRACTIONf_chiral_restr0.0541019
X-RAY DIFFRACTIONf_plane_restr0.0061123
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.15250.28621340.2372415194
2.1525-2.21070.24051380.2215427498
2.2107-2.27580.43791140.3603364482
2.2758-2.34920.24991420.20184404100
2.3492-2.43320.26531430.19634418100
2.4332-2.53060.26641420.19434419100
2.5306-2.64580.26821430.1944405100
2.6458-2.78520.24341410.18844409100
2.7852-2.95970.24681440.18564460100
2.9597-3.18820.22321440.18624457100
3.1882-3.50890.21071440.16924462100
3.5089-4.01640.20221450.1666443799
4.0164-5.05910.19731460.1474554100
5.0591-45.2950.22971520.1776470399
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)
13.2974-1.6251-0.58071.91750.40930.43330.03320.0978-0.1746-0.0219-0.06120.27340.0316-0.06250.0330.2167-0.02550.00120.17590.03140.218271.6289126.5806184.7394
21.9165-1.6039-0.34033.64670.80470.68460.17110.2097-0.1521-0.2999-0.14220.032-0.02390.0051-0.02880.23880.0004-0.0010.214-0.00520.19986.3761125.2772175.8224
30.95150.5977-0.18441.2066-0.43861.01060.06370.09660.0621-0.10490.02580.0166-0.07810.0171-0.08680.26220.0120.04610.1736-0.02070.267581.0113158.3548173.1245
41.40480.5724-0.38142.82160.5241.8874-0.13720.0957-0.2869-0.45550.1781-0.44640.28080.222-0.05480.40720.05650.03110.32050.01080.269397.6265143.4937153.222
54.3851-0.522-0.79082.47142.40852.6447-0.13720.3528-0.1298-0.30490.19050.55050.2725-0.0093-0.07780.5242-0.0034-0.06560.28660.06340.281681.1726145.2517147.4281
60.276-0.252-1.17073.2209-0.85826.44050.02531.0669-0.0188-0.62450.19750.2795-0.66460.1185-0.26370.66920.0305-0.0660.78370.06590.340482.0599143.8309142.7346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 214 )A1 - 214
2X-RAY DIFFRACTION2chain 'A' and (resid 215 through 364 )A215 - 364
3X-RAY DIFFRACTION3chain 'A' and (resid 365 through 552 )A365 - 552
4X-RAY DIFFRACTION4chain 'A' and (resid 553 through 756 )A553 - 756
5X-RAY DIFFRACTION5chain 'T' and (resid 5 through 18 )T5 - 18
6X-RAY DIFFRACTION6chain 'P' and (resid 1 through 11 )P1 - 11

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more