[English] 日本語
Yorodumi
- PDB-6kkj: Crystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kkj
TitleCrystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB, in the inward open conformation
ComponentsSugar efflux transporter
KeywordsPROTEIN TRANSPORT / MFS / Transporter protein
Function / homology
Function and homology information


transmembrane transporter activity / carbohydrate transmembrane transporter activity / transmembrane transport / plasma membrane
Similarity search - Function
Sugar efflux transporter, putative / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Sugar efflux transporter
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.385 Å
AuthorsXiao, Q.J. / Deng, D.
Funding support China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)YFA052700 China
National Science Foundation (NSF, China)JQ007 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Visualizing the nonlinear changes of a drug-proton antiporter from inward-open to occluded state.
Authors: Xiao, Q. / Sun, B. / Zhou, Y. / Wang, C. / Guo, L. / He, J. / Deng, D.
History
DepositionJul 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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
B: Sugar efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1043
Polymers45,4911
Non-polymers6132
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint3 kcal/mol
Surface area15440 Å2
Unit cell
Length a, b, c (Å)69.227, 89.150, 90.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Sugar efflux transporter


Mass: 45490.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: sotB, ydeA, b1528, JW1521 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31122
#2: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.71 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12% PEG 4000, 0.1 M Hepes pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.385→30 Å / Num. obs: 8067 / % possible obs: 98.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.055 / Rrim(I) all: 0.126 / Χ2: 0.884 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.4-3.523.20.5167800.6270.3220.6120.30496.8
3.52-3.663.70.477810.6690.2690.5440.32697.7
3.66-3.834.10.4047730.7890.2170.4610.39298.5
3.83-4.034.30.3037910.9060.1590.3430.47698.6
4.03-4.284.50.2077950.9780.1050.2330.71298.5
4.28-4.614.50.187930.9720.0910.2020.89599
4.61-5.075.10.1528160.9740.0730.1691.16599.6
5.07-5.85.30.1478160.980.0680.1631.06799.4
5.8-7.294.90.1148250.9890.0540.1261.29699.5
7.29-305.30.0858970.9930.040.0941.3999.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KKI

6kki


Resolution: 3.385→28.799 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 35.56
RfactorNum. reflection% reflection
Rfree0.287 802 9.98 %
Rwork0.2492 --
obs0.2529 8038 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 285.64 Å2 / Biso mean: 126.5292 Å2 / Biso min: 64.95 Å2
Refinement stepCycle: final / Resolution: 3.385→28.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 0 42 0 2664
Biso mean--140.2 --
Num. residues----357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.385-3.59670.42531250.3757114294
3.5967-3.87380.32281360.2841117399
3.8738-4.26250.28411280.2048119198
4.2625-4.87670.22861300.1834120999
4.8767-6.13430.26661380.26741217100
6.1343-28.7990.28991450.25231304100

+
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