[English] 日本語
Yorodumi
- PDB-7l16: Crystal structure of sugar-bound melibiose permease MelB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l16
TitleCrystal structure of sugar-bound melibiose permease MelB
ComponentsMelibiose carrier protein
KeywordsTRANSPORT PROTEIN / MFS-fold / galactoside binding / secondary active transport / MelB
Function / homology
Function and homology information


: / symporter activity / sodium ion transport / carbohydrate transport / plasma membrane
Similarity search - Function
Sodium:galactoside symporter / Sodium:galactoside symporter, conserved site / Sodium:galactoside symporter family signature. / MFS/sugar transport protein / Lactose permease-like / MFS transporter superfamily
Similarity search - Domain/homology
Dodecyl melibioside / Chem-LMO / Melibiose permease
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsGuan, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122759 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R21NS105863 United States
CitationJournal: Commun Biol / Year: 2021
Title: X-ray crystallography reveals molecular recognition mechanism for sugar binding in a melibiose transporter MelB.
Authors: Guan, L. / Hariharan, P.
History
DepositionDec 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Melibiose carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6032
Polymers54,0921
Non-polymers5111
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.372, 127.372, 103.905
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein Melibiose carrier protein / Melibiose permease / Melibiose transporter / Na+ (Li+)/melibiose symporter / Thiomethylgalactoside permease II


Mass: 54092.496 Da / Num. of mol.: 1 / Mutation: D59C, M5L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Cell line: LT2 / Gene: melB, STM4299 / Plasmid: pK95 / Details (production host): pK95 / Production host: Escherichia coli (E. coli) / Strain (production host): DW2 / Variant (production host): melBlacYZ / References: UniProt: P30878
#2: Sugar ChemComp-LMO / dodecyl 6-O-alpha-D-galactopyranosyl-beta-D-glucopyranoside / DDMB / dodecyl melibioside


Type: saccharide, Polysaccharide / Class: Protein binding / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / References: Dodecyl melibioside
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.62 Å3/Da / Density % sol: 73.35 % / Description: Rod
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50 mM BaCl2, 50 mM CaCl2, 100 mM Tris-HCl, pH 8.5, 29-32% PEG 400, 0.015% DDMB, 10% PEG3350
PH range: 6.5 - 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: May 19, 2018
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 3.15→29.35 Å / Num. obs: 16973 / % possible obs: 99.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 96.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.046 / Rrim(I) all: 0.146 / Χ2: 1.12 / Net I/σ(I): 18.2
Reflection shellResolution: 3.15→3.37 Å / Rmerge(I) obs: 1.1463 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3080 / CC1/2: 0.788 / Rpim(I) all: 0.477 / Rrim(I) all: 1.539 / Χ2: 0.89 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIXdev_3936refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MelB D59C with aNPG submitted

Resolution: 3.15→29.35 Å / SU ML: 0.3867 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2977 1706 10.05 %
Rwork0.273 15267 -
obs0.2754 16973 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.07 Å2
Refinement stepCycle: LAST / Resolution: 3.15→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3561 0 35 0 3596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223690
X-RAY DIFFRACTIONf_angle_d0.51965021
X-RAY DIFFRACTIONf_chiral_restr0.0363594
X-RAY DIFFRACTIONf_plane_restr0.003602
X-RAY DIFFRACTIONf_dihedral_angle_d4.066506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.240.33141410.32831275X-RAY DIFFRACTION100
3.24-3.350.34321410.30721265X-RAY DIFFRACTION100
3.35-3.470.37471440.34871258X-RAY DIFFRACTION99.86
3.47-3.610.3021370.34391239X-RAY DIFFRACTION98.29
3.61-3.770.45911310.39491179X-RAY DIFFRACTION91.87
3.77-3.970.34341400.3291240X-RAY DIFFRACTION96.71
3.97-4.210.29581450.2941286X-RAY DIFFRACTION100
4.22-4.540.26311440.25771256X-RAY DIFFRACTION100
4.54-4.990.2941400.23961308X-RAY DIFFRACTION100
5-5.710.31481470.25671289X-RAY DIFFRACTION100
5.72-7.180.29331460.27881319X-RAY DIFFRACTION100
7.19-29.350.23721500.21611353X-RAY DIFFRACTION99.27
Refinement TLS params.Method: refined / Origin x: -25.0960065607 Å / Origin y: 50.6654286047 Å / Origin z: -6.13688007058 Å
111213212223313233
T0.41567135325 Å2-0.0680571046813 Å20.0731099531072 Å2-0.944274917607 Å20.0258822111584 Å2--0.965852973239 Å2
L3.51835974773 °20.777601573742 °20.228352149364 °2-1.99528215542 °20.181240589999 °2--2.77104435704 °2
S0.326261581689 Å °0.316268203049 Å °0.0765050361261 Å °0.0761976944845 Å °-0.171240306407 Å °0.0786933747564 Å °0.141647854216 Å °0.0168170717582 Å °-0.151223237634 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://pdbjlvh1.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