[English] 日本語
Yorodumi
- PDB-7yll: Crystal structure of TTEDbh -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yll
TitleCrystal structure of TTEDbh
ComponentsDNA polymerase IV
KeywordsTRANSFERASE / polymerase of DinB subfamily / translesion synthesis / DNA binding protein / REPLICATION
Function / homology
Function and homology information


oxidized DNA binding / DNA synthesis involved in DNA repair / error-prone translesion synthesis / DNA-templated DNA replication / double-stranded DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm
Similarity search - Function
: / DNA polymerase-iota, thumb domain / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. ...: / DNA polymerase-iota, thumb domain / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / DNA polymerase IV
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.60000921196 Å
AuthorsYan, X. / Tian, L. / Gao, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structure and function of extreme TLS DNA polymerase TTEDbh from Thermoanaerobacter tengcongensis.
Authors: Tian, L.F. / Gao, H. / Yang, S. / Liu, Y.P. / Li, M. / Xu, W. / Yan, X.X.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1083
Polymers43,9881
Non-polymers1192
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-17 kcal/mol
Surface area17420 Å2
Unit cell
Length a, b, c (Å)105.196, 105.196, 74.211
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-532-

HOH

21A-646-

HOH

-
Components

#1: Protein DNA polymerase IV / Pol IV


Mass: 43988.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: dinB, TTE0254 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P58965, DNA-directed DNA polymerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 500 mM NaCl, 5 mM Mg3(PO4)2, 18% [w/v] PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97929 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.6→14.88 Å / Num. obs: 22314 / % possible obs: 98.2 % / Redundancy: 7.1 % / Biso Wilson estimate: 46.7017201672 Å2 / CC1/2: 0.98 / Net I/σ(I): 133.9
Reflection shellResolution: 2.6→2.77 Å / Num. unique obs: 2185 / CC1/2: 0.998

-
Processing

Software
NameVersionClassification
PHENIX1.12-2829_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RDI

2rdi


Resolution: 2.60000921196→14.8769609907 Å / SU ML: 0.310977302148 / Cross valid method: FREE R-VALUE / σ(F): 1.33649243903 / Phase error: 26.6724387516
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.265306133501 662 5.00832198517 %
Rwork0.229796337959 12556 -
obs0.231538208837 13218 99.9395130803 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.012083344 Å2
Refinement stepCycle: LAST / Resolution: 2.60000921196→14.8769609907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2589 0 6 162 2757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008206622205972637
X-RAY DIFFRACTIONf_angle_d1.396558012973561
X-RAY DIFFRACTIONf_chiral_restr0.0807025188084415
X-RAY DIFFRACTIONf_plane_restr0.00867601648747447
X-RAY DIFFRACTIONf_dihedral_angle_d24.91034268611003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.601-2.79950.357084946061460.2693100402722447X-RAY DIFFRACTION100
2.7995-3.0790.3736144207831220.2831768551542465X-RAY DIFFRACTION99.9613601236
3.079-3.51940.3129363807181220.2507999489682493X-RAY DIFFRACTION99.9617737003
3.5194-4.41480.2217089795151270.210841131172518X-RAY DIFFRACTION99.9622071051
4.4148-14.87690.2214883373791450.208236566562633X-RAY DIFFRACTION99.820337765

+
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