[English] 日本語
Yorodumi
- PDB-6fmg: Structure of the Mannose Transporter IIA Domain from Streptococcu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fmg
TitleStructure of the Mannose Transporter IIA Domain from Streptococcus pneumoniae
ComponentsPTS system mannose-specific transporter subunit IIAB
KeywordsTRANSFERASE / PTS / mannose transporter
Function / homology
Function and homology information


protein-Npi-phosphohistidine-D-mannose phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / membrane => GO:0016020 / kinase activity / plasma membrane / cytoplasm
Similarity search - Function
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 superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile.
Similarity search - Domain/homology
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMagoch, M. / Grudnik, P.
CitationJournal: To Be Published
Title: Structure of the Mannose Transporter IIA Domain from Streptococcus pneumoniae
Authors: Magoch, M. / Grudnik, P. / Nogly, P. / Dubin, G. / Archer, M. / Ma, P.
History
DepositionJan 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PTS system mannose-specific transporter subunit IIAB
B: PTS system mannose-specific transporter subunit IIAB
C: PTS system mannose-specific transporter subunit IIAB
D: PTS system mannose-specific transporter subunit IIAB


Theoretical massNumber of molelcules
Total (without water)60,1884
Polymers60,1884
Non-polymers00
Water8,323462
1
A: PTS system mannose-specific transporter subunit IIAB
D: PTS system mannose-specific transporter subunit IIAB


Theoretical massNumber of molelcules
Total (without water)30,0942
Polymers30,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-35 kcal/mol
Surface area11750 Å2
MethodPISA
2
B: PTS system mannose-specific transporter subunit IIAB
C: PTS system mannose-specific transporter subunit IIAB


Theoretical massNumber of molelcules
Total (without water)30,0942
Polymers30,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-38 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.528, 138.528, 69.767
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein
PTS system mannose-specific transporter subunit IIAB


Mass: 15047.067 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: manL_2, ERS020456_01132 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0T8BTT4, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium acetate tetrahydrate 0.1 M Sodium cacodylate 6.5 20 % w/v PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→49.15 Å / Num. obs: 1461081 / % possible obs: 100 % / Redundancy: 20.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.147 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10.5 % / Rmerge(I) obs: 2.052 / CC1/2: 0.666 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PDO

1pdo


Resolution: 1.8→26.179 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1965 3652 5.17 %
Rwork0.1702 67037 -
obs0.1716 70689 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.3 Å2 / Biso mean: 32.1307 Å2 / Biso min: 14.44 Å2
Refinement stepCycle: final / Resolution: 1.8→26.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4200 0 0 462 4662
Biso mean---38.7 -
Num. residues----560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114276
X-RAY DIFFRACTIONf_angle_d1.0885788
X-RAY DIFFRACTIONf_chiral_restr0.065648
X-RAY DIFFRACTIONf_plane_restr0.007772
X-RAY DIFFRACTIONf_dihedral_angle_d11.0792584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82370.33661500.303725592709100
1.8237-1.84870.30891360.282925492685100
1.8487-1.87510.29191490.271625702719100
1.8751-1.90310.27111320.245525622694100
1.9031-1.93280.24331220.228625822704100
1.9328-1.96450.25751300.213325812711100
1.9645-1.99830.21121350.207325472682100
1.9983-2.03460.23981570.197125612718100
2.0346-2.07380.22361440.194925842728100
2.0738-2.11610.22851090.197625952704100
2.1161-2.16210.22521450.188225452690100
2.1621-2.21230.20961380.179225652703100
2.2123-2.26760.20691290.159425872716100
2.2676-2.32890.18911300.164325932723100
2.3289-2.39740.21031440.159525842728100
2.3974-2.47470.20781390.16825642703100
2.4747-2.56310.2041430.16525672710100
2.5631-2.66560.21781650.168125712736100
2.6656-2.78680.21791430.17825572700100
2.7868-2.93360.18841700.170925612731100
2.9336-3.11710.19811260.175725902716100
3.1171-3.35730.22861140.178426132727100
3.3573-3.69430.18991420.148126162758100
3.6943-4.2270.14451630.134825702733100
4.227-5.31820.14211420.12626292771100
5.3182-26.18210.1681550.17132635279099

+
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