[English] 日本語
Yorodumi
- PDB-7b08: TgoT apo -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7b08
TitleTgoT apo
ComponentsDNA polymerase
KeywordsDNA BINDING PROTEIN / archaea / polymerase
Function / homology
Function and homology information


exonuclease activity / 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-directed DNA polymerase, family B, multifunctional 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 polymerase, palm domain superfamily / DNA polymerase type-B family ...: / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional 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 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
TRIETHYLENE GLYCOL / THYMIDINE-5'-TRIPHOSPHATE / DNA polymerase
Similarity search - Component
Biological speciesThermococcus gorgonarius (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.394 Å
AuthorsSamson, C. / Legrand, P. / Tekpinar, M. / Rozenski, J. / Abramov, M. / Holliger, P. / Pinheiro, V. / Herdewijn, P. / Delarue, M.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)G0H7618N Belgium
CitationJournal: Biomolecules / Year: 2020
Title: Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution.
Authors: Samson, C. / Legrand, P. / Tekpinar, M. / Rozenski, J. / Abramov, M. / Holliger, P. / Pinheiro, V.B. / Herdwijn, P. / Delarue, M.
History
DepositionNov 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5543
Polymers89,9211
Non-polymers6322
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-0 kcal/mol
Surface area36150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.060, 105.220, 152.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA polymerase / TO POL


Mass: 89921.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus gorgonarius (archaea) / Gene: pol, polA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P56689, DNA-directed DNA polymerase
#2: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 20K and 0.1 M MES-NaOH pH 6.5

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.972 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.394→45.86 Å / Num. obs: 41950 / % possible obs: 99.28 % / Redundancy: 2.5 % / Biso Wilson estimate: 79.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1222 / Net I/σ(I): 11.45
Reflection shellResolution: 2.394→2.48 Å / Rmerge(I) obs: 4.034 / Num. unique obs: 3986 / CC1/2: 0.287

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER2.10.3 (20-MAY-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tgo

1tgo


Resolution: 2.394→45.86 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.345 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.334 / SU Rfree Blow DPI: 0.234 / SU Rfree Cruickshank DPI: 0.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2612 2098 5 %RANDOM
Rwork0.2406 ---
obs0.2416 41950 99.5 %-
Displacement parametersBiso max: 198.04 Å2 / Biso min: 41.48 Å2
Baniso -1Baniso -2Baniso -3
1--7.4988 Å20 Å20 Å2
2--14.8123 Å20 Å2
3----7.3135 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: final / Resolution: 2.394→45.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 0 23 57 6174
Biso mean--156.24 67.59 -
Num. residues----742
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2256SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1040HARMONIC5
X-RAY DIFFRACTIONt_it6251HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion786SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4503SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6251HARMONIC20.005
X-RAY DIFFRACTIONt_angle_deg8425HARMONIC20.75
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion17.04
LS refinement shellResolution: 2.394→2.41 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3144 42 5.01 %
Rwork0.2926 797 -
obs--82.67 %
Refinement TLS params.

T11: 0.304 Å2 / 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 °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5049-1.08840.93973.89821.70453.3840.0226-0.17080.15280.54420.2311-0.54420.04020.1607-0.2536-0.0398-0.1325-0.3035-0.0143-0.2029-1.5267-4.020145.7575
23.3444-0.44920.51478.3155-0.93127.8315-0.23030.36080.4968-0.5312-0.08370.1321-0.52280.0490.3140.0009-0.152-0.16050.041-0.03-17.750113.735215.7848
30.4278-1.0684-0.1022.78450.651.55370.03430.13330.0217-0.1375-0.0879-0.3261-0.0980.10830.0536-0.0657-0.0359-0.19540.0247-0.175-1.8901-21.788621.2452
43.95721.0485-1.89877.1707-0.8558.31550.04320.37040.27790.54420.32460.5442-0.1939-0.5442-0.36780.0188-0.0185-0.07370.1112-0.1368-4.6808-30.6758-1.2529
50.88071.192-1.0038.3155-1.57226.36280.1497-0.11810.54420.00670.1964-0.1073-0.5442-0.2278-0.34620.06670.08410.13040.07630.2759-0.4237-1.5515-18.617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|131 }A1 - 131
2X-RAY DIFFRACTION2{ A|132 - A|327 }A132 - 327
3X-RAY DIFFRACTION3{ A|328 - A|532 A|801 }A328 - 532
4X-RAY DIFFRACTION3{ A|328 - A|532 A|801 }A801
5X-RAY DIFFRACTION4{ A|533 - A|610 }A533 - 610
6X-RAY DIFFRACTION5{ A|612 - A|757 }A612 - 757

+
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