[English] 日本語
Yorodumi
- PDB-4gc0: The structure of the MFS (major facilitator superfamily) proton:x... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gc0
TitleThe structure of the MFS (major facilitator superfamily) proton:xylose symporter XylE bound to 6-bromo-6-deoxy-D-glucose
ComponentsD-xylose-proton symporter
KeywordsTRANSPORT PROTEIN / MFS / D-xylose:proton symporter
Function / homology
Function and homology information


D-xylose:proton symporter activity / D-xylose transmembrane transport / transmembrane transporter activity / transmembrane transport / membrane / plasma membrane
Similarity search - Function
: / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Major facilitator, sugar transporter-like / Sugar (and other) transporter / MFS general substrate transporter like domains / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. ...: / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Major facilitator, sugar transporter-like / Sugar (and other) transporter / MFS general substrate transporter like domains / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
6-bromo-6-deoxy-beta-D-glucopyranose / D-xylose-proton symporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYan, N. / Sun, L.F. / Zeng, X. / Yan, C.Y.
CitationJournal: Nature / Year: 2012
Title: Crystal structure of a bacterial homologue of glucose transporters GLUT1-4.
Authors: Sun, L. / Zeng, X. / Yan, C. / Sun, X. / Gong, X. / Rao, Y. / Yan, N.
History
DepositionJul 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-xylose-proton symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1116
Polymers53,6431
Non-polymers1,4695
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.171, 95.171, 171.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein D-xylose-proton symporter


Mass: 53642.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: xylE, b4031, JW3991 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AGF4
#2: Sugar ChemComp-6BG / 6-bromo-6-deoxy-beta-D-glucopyranose / 6-bromo-6-deoxy-beta-D-glucose / 6-bromo-6-deoxy-D-glucose / 6-bromo-6-deoxy-glucose


Type: D-saccharide, beta linking / Mass: 243.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11BrO5
IdentifierTypeProgram
b-D-Glcp6bromoIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.62 Å3/Da / Density % sol: 66.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.6
Details: 40 % (w/v) PEG400, 0.05 M Glycine pH 9.6 and 0.1 M LiCl , VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9196 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 25081 / Num. obs: 24981 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.6→2.69 Å / % possible all: 97.9

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GBY

4gby


Resolution: 2.6→39.123 Å / SU ML: 0.28 / σ(F): 1.12 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1241 4.98 %RANDOM
Rwork0.2271 ---
all0.2281 25021 --
obs0.2281 24914 99.57 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.919 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.736 Å2-0 Å20 Å2
2---18.736 Å2-0 Å2
3---24.0673 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 96 7 3728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123816
X-RAY DIFFRACTIONf_angle_d1.3245187
X-RAY DIFFRACTIONf_dihedral_angle_d17.5541337
X-RAY DIFFRACTIONf_chiral_restr0.083609
X-RAY DIFFRACTIONf_plane_restr0.009625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.65560.35531390.30742679X-RAY DIFFRACTION96
2.6556-2.71730.30171210.2982764X-RAY DIFFRACTION100
2.7173-2.78530.35181280.28542780X-RAY DIFFRACTION100
2.7853-2.86050.28761350.26322755X-RAY DIFFRACTION100
2.8605-2.94470.27851230.26452766X-RAY DIFFRACTION100
2.9447-3.03970.33141560.25712752X-RAY DIFFRACTION100
3.0397-3.14830.27141170.26132761X-RAY DIFFRACTION100
3.1483-3.27430.31841700.25552748X-RAY DIFFRACTION100
3.2743-3.42320.22941390.23272758X-RAY DIFFRACTION100
3.4232-3.60360.2361660.22262708X-RAY DIFFRACTION100
3.6036-3.82920.2311550.21962748X-RAY DIFFRACTION100
3.8292-4.12450.21411550.21622770X-RAY DIFFRACTION100
4.1245-4.5390.2071550.18822734X-RAY DIFFRACTION100
4.539-5.19460.23051680.19352728X-RAY DIFFRACTION100
5.1946-6.53960.2581510.25352741X-RAY DIFFRACTION100
6.5396-39.12750.24261240.21732695X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -27.2331 Å / Origin y: 21.9288 Å / Origin z: -3.9812 Å
111213212223313233
T0.5767 Å20.0811 Å20.0035 Å2-0.4871 Å20.0054 Å2--0.4825 Å2
L2.5783 °2-0.3198 °2-0.7292 °2-2.0187 °20.2669 °2--1.59 °2
S-0.1941 Å °-0.2515 Å °-0.1865 Å °0.2777 Å °0.1943 Å °-0.2985 Å °0.1114 Å °0.1199 Å °-0.0294 Å °
Refinement TLS groupSelection details: all

+
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