[English] 日本語
Yorodumi
- PDB-1pdo: PHOSPHOENOLPYRUVATE-DEPENDENT PHOSPHOTRANSFERASE SYSTEM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pdo
TitlePHOSPHOENOLPYRUVATE-DEPENDENT PHOSPHOTRANSFERASE SYSTEM
ComponentsMANNOSE PERMEASE
KeywordsPHOSPHOTRANSFERASE / PHOSPHOENOLPYRUVATE DEPENDENT PHOSPHOTRANSFERASE SYSTEM
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / protein homodimerization activity / membrane ...protein-Npi-phosphohistidine-D-mannose phosphotransferase / mannose transmembrane transport / protein-N(PI)-phosphohistidine-mannose phosphotransferase system transporter activity / glucose import across plasma membrane / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / protein homodimerization activity / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phosphotransferase system, mannose family IIA component / Phosphotransferase system, sorbose subfamily IIB component, subgroup / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily ...Phosphotransferase system, mannose family IIA component / Phosphotransferase system, sorbose subfamily IIB component, subgroup / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system mannose-specific EIIAB component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS SOFTWARE USED : CCP4 PROGRAM SUITE 1994 STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL / Resolution: 1.7 Å
AuthorsNunn, R.S. / Erni, B. / Schirmer, T.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Structure of the IIA domain of the mannose transporter from Escherichia coli at 1.7 angstroms resolution.
Authors: Nunn, R.S. / Markovic-Housley, Z. / Genovesio-Taverne, J.C. / Flukiger, K. / Rizkallah, P.J. / Jansonius, J.N. / Schirmer, T. / Erni, B.
#1: Journal: J.Biol.Chem. / Year: 1987
Title: The Mannose Permease of Escherichia Coli Consists of Three Different Proteins. Amino Acid Sequence and Function in Sugar Transport, Sugar Phosphorylation, and Penetration of Phage Lambda DNA
Authors: Erni, B. / Zanolari, B. / Kocher, H.P.
History
DepositionMar 8, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 21, 2020Group: Advisory / Data collection / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / reflns_shell
Item: _pdbx_database_status.process_site / _reflns_shell.Rmerge_I_obs
Revision 1.4Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MANNOSE PERMEASE


Theoretical massNumber of molelcules
Total (without water)14,6251
Polymers14,6251
Non-polymers00
Water1,26170
1
A: MANNOSE PERMEASE

A: MANNOSE PERMEASE


Theoretical massNumber of molelcules
Total (without water)29,2492
Polymers29,2492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area3370 Å2
ΔGint-29 kcal/mol
Surface area10640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.360, 76.360, 88.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-181-

HOH

-
Components

#1: Protein MANNOSE PERMEASE / MANNOSE TRANSPORTER / IIAB SUBUNIT


Mass: 14624.625 Da / Num. of mol.: 1
Fragment: IIA ==MAN== DOMAIN, RESIDUES 2 - 133, OF THE IIAB ==MAN== SUBUNIT PLUS PHE-ALA-GLY AT THE CARBOXY TERMINUS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12-RP7029
Description: SUBCLONAL IIA COMPRISES RESIDUES 1 - 133 OF THE WILD-TYPE IIAB SEQUENCE PLUS PHE-ALA-GLY AT THE CARBOXY TERMINUS. THE INITIAL SE-MET WAS REMOVED BY PROTEOLYTIC CLEAVAGE.
Plasmid: PJFL1320 / Species (production host): Escherichia coli / Gene (production host): MANX / Production host: Escherichia coli K12 (bacteria) / Strain (production host): WA2127 AND D41
References: UniProt: P69797, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDURING CATALYSIS HIS 10 GETS TRANSIENTLY PHOSPHORYLATED.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 46 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
19.3 mg/mlprotein1dropand 9.8 mg/ml
21.8 Mammonium sulfate1reservoir
310 mM1reservoirCoCl2
40.1 MMES1reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 3, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.7→19.8 Å / Num. obs: 16839 / % possible obs: 97.3 % / Observed criterion σ(I): 4 / Redundancy: 5.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 32.4
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 8.1 / % possible all: 95.8
Reflection shell
*PLUS
% possible obs: 95.8 %

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS SOFTWARE USED : CCP4 PROGRAM SUITE 1994 STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL
Resolution: 1.7→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.244 -10 %
Rwork0.189 --
obs0.189 16645 95.8 %
Displacement parametersBiso mean: 20.2 Å2
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 0 70 1058
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it22
X-RAY DIFFRACTIONx_mcangle_it33
X-RAY DIFFRACTIONx_scbond_it33
X-RAY DIFFRACTIONx_scangle_it44
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

+
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