[English] 日本語
Yorodumi
- SASDBZ5: Enzyme I-Ntr (residues 170-424) in complex with NPr (residues 1-85) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDBZ5
SampleEnzyme I-Ntr (residues 170-424) in complex with NPr (residues 1-85)
  • Phosphocarrier protein NPr (protein), NPr, Escherichia coli
  • Phosphoenolpyruvate-protein phosphotransferase PtsP (protein), Enzyme I-Ntr, Escherichia coli
Function / homology
Function and homology information


transferase activity, transferring phosphorus-containing groups / phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / response to organonitrogen compound / kinase activity / phosphorylation / metal ion binding / cytoplasm
Similarity search - Function
Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / PEP-utilising enzyme, N-terminal / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain ...Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / PEP-utilising enzyme, N-terminal / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / Phosphotransferase system, HPr histidine phosphorylation site / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily
Similarity search - Domain/homology
Phosphocarrier protein NPr / Phosphoenolpyruvate-dependent phosphotransferase system
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
CitationDate: 2016 Nov 8
Title: Structure of the NPr:EIN-Ntr Complex: Mechanism for Specificity in Paralogous Phosphotransferase Systems.
Authors: Strickland M / Stanley AM / Wang G / Botos I / Schwieters CD / Buchanan SK / Peterkofsky A
Contact author
  • Madeleine Strickland (NIH, National Institutes of Health, Bethesda, MD, Bethesda, Maryland, USA)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #893
Type: atomic / Software: CRYSOL (2.8.3) / Comment: Fig. 5J / Chi-square value: 1.248
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Enzyme I-Ntr (residues 170-424) in complex with NPr (residues 1-85)
Specimen concentration: 3.76 mg/ml / Entity id: 390 / 391
BufferName: 10 mM Tris 150 mM NaCl 0.5 mM EDTA / pH: 7.5
Entity #390Name: NPr / Type: protein / Description: Phosphocarrier protein NPr / Formula weight: 9.25 / Num. of mol.: 1 / Source: Escherichia coli / References: UniProt: P0A9N0
Sequence:
MTVKQTVEIT NKLGMHARPA MKLFELMQGF DAEVLLRNDE GTEAEANSVI ALLMLDSAKG RQIEVEATGP QEEEALAAVI ALFNS
Entity #391Name: Enzyme I-Ntr / Type: protein
Description: Phosphoenolpyruvate-protein phosphotransferase PtsP
Formula weight: 28.35 / Num. of mol.: 1 / Source: Escherichia coli / References: UniProt: P37177
Sequence: RIRALPAAPG VAIAEGWQDA TLPLMEQVYQ ASTLDPALER ERLTGALEEA ANEFRRYSKR FAAGAQKETA AIFDLYSHLL SDTRLRRELF AEVDKGSVAE WAVKTVIEKF AEQFAALSDN YLKERAGDLR ALGQRLLFHL DDANQGPNAW PERFILVADE LSATTLAELP ...Sequence:
RIRALPAAPG VAIAEGWQDA TLPLMEQVYQ ASTLDPALER ERLTGALEEA ANEFRRYSKR FAAGAQKETA AIFDLYSHLL SDTRLRRELF AEVDKGSVAE WAVKTVIEKF AEQFAALSDN YLKERAGDLR ALGQRLLFHL DDANQGPNAW PERFILVADE LSATTLAELP QDRLVGVVVR DGAANSHAAI MVRALGIPTV MGADIQPSVL HRRTLIVDGY RGELLVDPEP VLLQEYQRLI SEEIELSRLA EDDVN

-
Experimental information

BeamInstrument name: NIDDK, NIH / City: Bethesda, MD / 国: USA / Type of source: X-ray in house / Wavelength: 0.154 Å
Scan
Title: Enzyme I-Ntr (residues 170-424) in complex with NP / Measurement date: Jan 30, 2015 / Storage temperature: 4 °C / Cell temperature: 27 °C / Exposure time: 1800 sec. / Number of frames: 8 / Unit: 1/A /
MinMax
Q0.0181 0.6797
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 214 /
MinMax
Q0.032546 0.339536
P(R) point1 214
R0 81.56
Result
Type of curve: single_conc
ExperimentalStandardPorod
MW37.6 kDa22 kDa30.6 kDa
Volume--52 nm3

P(R)Guinier
Forward scattering, I02.87 2.83
Radius of gyration, Rg2.373 nm2.319 nm

MinMax
D-8.16
Guinier point7 25

+
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