[English] 日本語
Yorodumi
- PDB-9k3e: DddB(BadTF3) dsDNA deaminase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9k3e
TitleDddB(BadTF3) dsDNA deaminase
Components
  • The immunity protein of DddB
  • YD repeat protein
KeywordsHYDROLASE / DsDNA deaminase
Function / homology
Function and homology information


Pput2613-like deaminase / Pput_2613-like deaminase / Bacteriophage T4 gp5 C-terminal trimerisation domain / Type VI secretion system, RhsGE-associated Vgr family subset / Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / RHS repeat / RHS Repeat ...Pput2613-like deaminase / Pput_2613-like deaminase / Bacteriophage T4 gp5 C-terminal trimerisation domain / Type VI secretion system, RhsGE-associated Vgr family subset / Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / RHS repeat / RHS Repeat / Type VI secretion system, RhsGE-associated Vgr protein / Phage tail baseplate hub (GPD) / YD repeat / Gp5/Type VI secretion system Vgr protein, OB-fold domain / Type VI secretion system/phage-baseplate injector OB domain / Vgr protein, OB-fold domain superfamily / Rhs repeat-associated core / :
Similarity search - Domain/homology
YD repeat protein / Uncharacterized protein
Similarity search - Component
Biological speciesTaylorella equigenitalis
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDong, W.Y. / Xiaoliang, S.X.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Genome-wide mapping of human transcription factors' footprints with double-stranded DNA deaminase
Authors: Wenyang, D. / Xiaoliang, S.X.
History
DepositionOct 18, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: YD repeat protein
C: The immunity protein of DddB


Theoretical massNumber of molelcules
Total (without water)28,7332
Polymers28,7332
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-7 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.069, 130.646, 61.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein YD repeat protein


Mass: 15227.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taylorella equigenitalis (strain MCE9) (bacteria)
Gene: TEQUI_0434 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A654KG07
#2: Protein The immunity protein of DddB


Mass: 13505.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Taylorella equigenitalis (strain MCE9) (bacteria)
Gene: TEQUI_0433 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A654KG21
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10% (w/v) PEG 8000, 100 mM Potassium phosphate monobasic/ Sodium phosphate dibasic, 200 mM Sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→12.62 Å / Num. obs: 11988 / % possible obs: 99.94 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.025 / Rrim(I) all: 0.079 / Net I/σ(I): 25.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.298 / Num. unique obs: 1175 / Rpim(I) all: 0.101 / Rrim(I) all: 0.315

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PHENIXphasing
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→12.62 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1197 10 %
Rwork0.1944 --
obs0.1988 11971 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→12.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 0 82 1862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081815
X-RAY DIFFRACTIONf_angle_d0.9662457
X-RAY DIFFRACTIONf_dihedral_angle_d7.724242
X-RAY DIFFRACTIONf_chiral_restr0.058274
X-RAY DIFFRACTIONf_plane_restr0.007320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.27711310.21741181X-RAY DIFFRACTION99
2.6-2.720.34241300.22081173X-RAY DIFFRACTION100
2.72-2.860.25491310.23661174X-RAY DIFFRACTION100
2.86-3.030.26151320.23811184X-RAY DIFFRACTION100
3.04-3.270.27741320.2131188X-RAY DIFFRACTION100
3.27-3.590.25141320.19521191X-RAY DIFFRACTION100
3.59-4.090.23951350.17881210X-RAY DIFFRACTION100
4.09-5.10.191330.16311204X-RAY DIFFRACTION100
5.1-12.620.20311410.18211269X-RAY DIFFRACTION100

+
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