[English] 日本語
Yorodumi
- PDB-3ufb: Crystal structure of a modification subunit of a putative type I ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ufb
TitleCrystal structure of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016
ComponentsType I restriction-modification system methyltransferase subunit
KeywordsTRANSFERASE / Methyltransferase activity
Function / homology
Function and homology information


N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / DNA binding
Similarity search - Function
N6 adenine-specific DNA methyltransferase, N-terminal domain / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal domain / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Ferritin / Vaccinia Virus protein VP39 ...N6 adenine-specific DNA methyltransferase, N-terminal domain / N6 adenine-specific DNA methyltransferase, N-terminal domain / Type I restriction enzyme EcoKI-like, methylase subunit, N-terminal domain superfamily / HsdM N-terminal domain / N-6 DNA Methylase / DNA methylase, adenine-specific / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Ferritin / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsPark, S.Y. / Lee, H.J. / Sun, J. / Nishi, K. / Song, J.M. / Kim, J.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural characterization of a modification subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016
Authors: Park, S.Y. / Lee, H.J. / Song, J.M. / Sun, J. / Hwang, H.J. / Nishi, K. / Kim, J.S.
History
DepositionNov 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type I restriction-modification system methyltransferase subunit


Theoretical massNumber of molelcules
Total (without water)60,2261
Polymers60,2261
Non-polymers00
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.899, 78.899, 165.802
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

21A-629-

HOH

-
Components

#1: Protein Type I restriction-modification system methyltransferase subunit


Mass: 60226.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: YJ016 / Gene: VV0266 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7MPU6, site-specific DNA-methyltransferase (adenine-specific)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1442.58
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, hanging drop7.520 % (w/v) polyethylene glycol 8,000, 0.1 M at Hepes pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
2912vapor diffusion, hanging drop7.524 % (w/v) polyethyleneglycol 3350, 0.1 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid at pH 7.5 and 10 mM -mercaptoethanol , VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction
IDCrystal-ID
11
22
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A11
SYNCHROTRONALS 8.3.120.98962
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDNov 12, 2008
ADSC QUANTUM 315r2CCDSep 1, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.989621
ReflectionResolution: 1.8→50 Å / Num. obs: 48972 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→5.999 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8892 / SU ML: 0.18 / σ(F): 0.1 / Phase error: 18.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2154 4811 10.11 %
Rwork0.1809 --
obs0.1844 47581 99.46 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.195 Å2 / ksol: 0.6 e/Å3
Displacement parametersBiso max: 92.89 Å2 / Biso mean: 29.2993 Å2 / Biso min: 10.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.9082 Å2-0 Å20 Å2
2---2.9082 Å20 Å2
3---5.8163 Å2
Refinement stepCycle: LAST / Resolution: 1.8→5.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 0 542 4398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073936
X-RAY DIFFRACTIONf_angle_d1.0065317
X-RAY DIFFRACTIONf_dihedral_angle_d13.7611500
X-RAY DIFFRACTIONf_chiral_restr0.069569
X-RAY DIFFRACTIONf_plane_restr0.004707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.81990.29221450.28140399
1.8199-1.84070.29571480.2622139999
1.8407-1.86250.2991570.2486139699
1.8625-1.88540.28341740.234137999
1.8854-1.90940.26881330.24431425100
1.9094-1.93470.25751650.2213141499
1.9347-1.96140.26661590.2177139799
1.9614-1.98960.26521830.2182137599
1.9896-2.01950.23721700.19821421100
2.0195-2.05130.23751640.19781380100
2.0513-2.08530.22981640.18811437100
2.0853-2.12150.23291530.17791418100
2.1215-2.16050.22641790.17361393100
2.1605-2.20240.21081560.16391435100
2.2024-2.24780.19991520.16711406100
2.2478-2.29730.21361580.1637142399
2.2973-2.35130.20961560.1716144399
2.3513-2.41090.21571620.1754140599
2.4109-2.4770.21581540.1859143499
2.477-2.5510.23351490.1871144299
2.551-2.63470.24851830.1871398100
2.6347-2.73060.21581560.185143199
2.7306-2.84220.21811540.1817142499
2.8422-2.97450.22831620.1784143299
2.9745-3.13570.19751520.1732146299
3.1357-3.33850.21141450.17361470100
3.3385-3.60670.19561800.15871463100
3.6067-3.98920.18991750.15511453100
3.9892-4.61230.15731610.15811490100
4.6123-5.99950.20731620.18381522100

+
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