[English] 日本語
Yorodumi
- SASDCB7: Streptococcus pneumoniae phosphodiesterase Pde2 (DHH subfamily 1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDCB7
SampleStreptococcus pneumoniae phosphodiesterase Pde2
  • DHH subfamily 1 protein (protein), SpnPde2, Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)
Function / homology: / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / nucleic acid binding / DHH subfamily 1 protein
Function and homology information
Biological speciesStreptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
CitationDate: 2017 Oct
Title: Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima
Authors: Drexler D / Müller M / Rojas-Cordova C / Bandera A
Contact author
  • Gregor Witte (Ludwig-Maximilians-Universität München)

-
Structure visualization

Downloads & links

-
Models

-
Sample

SampleName: Streptococcus pneumoniae phosphodiesterase Pde2 / Specimen concentration: 7 mg/ml
BufferName: 20mM Tris, 200 mM NaCl, 5%(v/v) glycerol / pH: 7.5
Entity #737Name: SpnPde2 / Type: protein / Description: DHH subfamily 1 protein / Formula weight: 35.053 / Num. of mol.: 2
Source: Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)
References: UniProt: A0A0H2ZNP2
Sequence: SMEICQQILE KIKEYDTIII HRHMKPDPDA LGSQVGLKAL LEHHFPEKTI KAVGFDEPTL TWMAEMDLVE DRAYQGALVI VCDTANTARI DDKRYSQGDF LIKIDHHPND DVYGDLSWVD TSSSSASEMI TLFAQTTQLA LADRDAELLF AGIVGDTGRF LYPSTTARTL ...Sequence:
SMEICQQILE KIKEYDTIII HRHMKPDPDA LGSQVGLKAL LEHHFPEKTI KAVGFDEPTL TWMAEMDLVE DRAYQGALVI VCDTANTARI DDKRYSQGDF LIKIDHHPND DVYGDLSWVD TSSSSASEMI TLFAQTTQLA LADRDAELLF AGIVGDTGRF LYPSTTARTL RLAAYLREHN FDFAALTRKM DTMSYKIAKL QGYIYDHLEV DENGAARVIL SQEVLKQYNV TDAETAAIVG APGRIDRVSL WGIFVEQADG HYRVRLRSKI HPINEIAKEH DGGGHPLASG ANSYSLEENE IIYQKLKNLL KN

-
Experimental information

BeamInstrument name: PETRA III P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.123987 Å / Dist. spec. to detc.: 3 mm
DetectorName: Pilatus 2M
Scan
Title: Streptococcus pneumoniae phosphodiesterase Pde2 / Measurement date: Jun 23, 2015 / Cell temperature: 20 °C / Exposure time: 0.045 sec. / Number of frames: 39 / Unit: 1/nm /
MinMax
Q0.0268 4.8081
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1104 /
MinMax
Q0.0610767 2.97316
P(R) point1 1104
R0 7.74
Result
Type of curve: single_conc /
ExperimentalPorod
MW57 kDa67 kDa
Volume-86.56 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I021410 13.4 21234 19.57
Radius of gyration, Rg2.72 nm0.148 2.69 nm0.23

MinMax
D-7.74
Guinier point14 146

+
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