[English] 日本語
Yorodumi
- PDB-3h1t: The fragment structure of a putative HsdR subunit of a type I res... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h1t
TitleThe fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016
ComponentsType I site-specific restriction-modification system, R (Restriction) subunit
KeywordsHYDROLASE / restriction enzyme hsdR / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


DNA modification / hydrolase activity / DNA binding / ATP binding
Similarity search - Function
EcoEI R protein C-terminal domain / Type I restriction enzyme R protein, N-terminal domain / EcoEI R protein C-terminal / Type I restriction enzyme R protein N terminus (HSDR_N) / tt1808, chain A - #30 / tt1808, chain A / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...EcoEI R protein C-terminal domain / Type I restriction enzyme R protein, N-terminal domain / EcoEI R protein C-terminal / Type I restriction enzyme R protein N terminus (HSDR_N) / tt1808, chain A - #30 / tt1808, chain A / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Type I site-specific restriction-modification system, R (Restriction) subunit
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPark, S.Y. / Lee, H.J. / Kim, J.S.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity
Authors: Uyen, N.T. / Park, S.Y. / Choi, J.W. / Lee, H.J. / Nishi, K. / Kim, J.S.
History
DepositionApr 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Derived calculations / Category: reflns / struct_conn
Item: _reflns.pdbx_Rmerge_I_obs / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type I site-specific restriction-modification system, R (Restriction) subunit


Theoretical massNumber of molelcules
Total (without water)68,0771
Polymers68,0771
Non-polymers00
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.244, 88.780, 114.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Type I site-specific restriction-modification system, R (Restriction) subunit


Mass: 68077.242 Da / Num. of mol.: 1 / Fragment: UNP residues 1-590
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: YJ016 / Gene: VV0265 / Plasmid: pProExHTc / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q7MPU7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8-10% polyethylene glycol3350, 0.15M NH4Cl, 0.1M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid at pH7.5, 2mM mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 2008 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 32645 / Num. obs: 31838 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.099 / Rsym value: 0.102 / Net I/σ(I): 11.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.42 / Num. unique all: 2808 / Rsym value: 0.422 / % possible all: 87.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→44.39 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 3167 -random
Rwork0.2182 ---
all0.221 32879 --
obs0.221 31603 96.1 %-
Refinement stepCycle: LAST / Resolution: 2.3→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 0 343 4519
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.008

+
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