[English] 日本語
Yorodumi
- PDB-1cm2: STRUCTURE OF HIS15ASP HPR AFTER HYDROLYSIS OF RINGED SPECIES. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cm2
TitleSTRUCTURE OF HIS15ASP HPR AFTER HYDROLYSIS OF RINGED SPECIES.
ComponentsHISTIDINE-CONTAINING PROTEIN
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / SUCCINIMIDE / ISOIMIDE
Function / homology
Function and homology information


phosphotransferase activity, nitrogenous group as acceptor / regulation of carbon utilization / antisigma factor binding / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / enzyme activator activity / enzyme regulator activity / cytosol
Similarity search - Function
Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / HPr-like / Histidine-containing Protein; Chain: A; / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNapper, S. / Delbaere, L.T.J. / Waygood, E.B.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: The aspartyl replacement of the active site histidine in histidine-containing protein, HPr, of the Escherichia coli Phosphoenolpyruvate:Sugar phosphotransferase system can accept and donate a ...Title: The aspartyl replacement of the active site histidine in histidine-containing protein, HPr, of the Escherichia coli Phosphoenolpyruvate:Sugar phosphotransferase system can accept and donate a phosphoryl group. Spontaneous dephosphorylation of acyl-phosphate autocatalyzes an internal cyclization
Authors: Napper, S. / Delbaere, L.T. / Waygood, E.B.
History
DepositionMay 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HISTIDINE-CONTAINING PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,1061
Polymers9,1061
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.920, 45.970, 27.220
Angle α, β, γ (deg.)90.00, 104.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein HISTIDINE-CONTAINING PROTEIN / PHOSPHOCARRIER PROTEIN HPR


Mass: 9106.273 Da / Num. of mol.: 1 / Mutation: HIS15ASP
Source method: isolated from a genetically manipulated source
Details: THE STRUCTURE IS THAT OF HIS15ASP HPR WHICH HAS UNDERGONE HYDROLYSIS FROM A HIGH-PI RINGED SPECIES OF THE PROTEIN WHICH IS BELIEVED TO INVOLVE SUCCINIMIDE OR ISOIMIDE FORMATION.
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PTSH / Plasmid: PUC19 / Cell line (production host): ESK108 / Gene (production host): PTSH / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA04
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 1.73 Å3/Da / Density % sol: 28.75 %
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 14 ℃ / pH: 4.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Mcitrate phosphate1reservoir
220-25 %satammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Type: PHOTON FACTORY / Wavelength: 1
DetectorType: WEISSENBERG
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 6570 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Rsym value: 9.7

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD TYPE E. COLI HPR

Resolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.2 --
obs0.2 6570 97.5 %
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms783 0 0 143 926
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.2 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 / Num. reflection obs: 5670
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.4

+
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