[English] 日本語
Yorodumi
- PDB-7klf: Ternary structure of Dpo4 bound to G in the template base paired ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7klf
TitleTernary structure of Dpo4 bound to G in the template base paired with incoming dCTP
Components
  • DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3')
  • DNA polymerase IV
KeywordsDNA BINDING PROTEIN / DNA polymerase
Function / homology
Function and homology information


error-prone translesion synthesis / DNA-templated DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm
Similarity search - Function
DNA polymerase type-Y, HhH motif / IMS family HHH motif / 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 type-Y, HhH motif / IMS family HHH motif / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase IV
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
Saccharolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.301 Å
AuthorsKoag, M.-C. / Lee, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES-26676 United States
CitationJournal: To Be Published
Title: Structure of human DNA polymerase beta complexed with 8OA in the template base paired with incoming non-hydrolyzable ATP
Authors: Koag, M.-C. / Lee, S.
History
DepositionOct 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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 IV
T: DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')
P: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3897
Polymers48,8023
Non-polymers5874
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-71 kcal/mol
Surface area20560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.520, 102.373, 52.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase IV / Pol IV


Mass: 39019.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: dbh, dpo4, SSO2448 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W02, DNA-directed DNA polymerase

-
DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA (5'-D(*CP*TP*AP*AP*CP*GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')


Mass: 5685.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharolobus solfataricus P2 (archaea)
#3: DNA chain DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3')


Mass: 4096.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharolobus solfataricus P2 (archaea)

-
Non-polymers , 3 types, 58 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 12 to 18% PEG 3350, 100 mM HEPES (pH 6.6),100 mM calcicum acetate, and 2.5% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 24689 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 41.13 Å2 / Rmerge(I) obs: 0.091 / Χ2: 1.214 / Net I/σ(I): 8.1 / Num. measured all: 263794
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.3-2.349.60.72512010.659199.9
2.34-2.3810.50.65812060.6591100
2.38-2.4310.80.57612130.671100
2.43-2.48110.50111910.6681100
2.48-2.53110.4412300.6861100
2.53-2.59110.39712130.7091100
2.59-2.6510.90.32612170.6951100
2.65-2.73110.28712070.7331100
2.73-2.8110.90.23412410.7561100
2.81-2.9110.20212080.7921100
2.9-310.90.16412250.8041100
3-3.1210.80.12612560.871100
3.12-3.2610.90.09512021.0181100
3.26-3.4310.80.08312441.2271100
3.43-3.6510.80.0812311.7231100
3.65-3.9310.70.08712472.5511100
3.93-4.3210.60.08212533.4431100
4.32-4.9310.40.06812682.8271100
4.93-6.1810.10.0512761.4411100
6.18-1010.10.03513601.263199.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QZ7

3qz7


Resolution: 2.301→19.538 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 1220 5.11 %
Rwork0.2312 22651 -
obs0.2335 23871 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 230.69 Å2 / Biso mean: 48.0753 Å2 / Biso min: 19.32 Å2
Refinement stepCycle: final / Resolution: 2.301→19.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 649 31 54 3477
Biso mean--35.8 46.3 -
Num. residues----373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033538
X-RAY DIFFRACTIONf_angle_d0.6284899
X-RAY DIFFRACTIONf_chiral_restr0.043557
X-RAY DIFFRACTIONf_plane_restr0.003505
X-RAY DIFFRACTIONf_dihedral_angle_d19.8962069
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3011-2.39270.40081160.294228390
2.3927-2.50140.34781500.2815236593
2.5014-2.63290.3271240.2796243095
2.6329-2.79750.35391340.2769246796
2.7975-3.01270.34311470.2839250698
3.0127-3.31460.29951360.26452599100
3.3146-3.79120.27691450.22852588100
3.7912-4.7650.25361340.20052648100
4.765-100.20761340.19072765100

+
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