[English] 日本語
Yorodumi
- PDB-5yck: Crystal structure of a MATE family protein derived from Camelina ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yck
TitleCrystal structure of a MATE family protein derived from Camelina sativa at 2.3 angstrom
Componentsmulti drug efflux transporter
KeywordsTRANSPORT PROTEIN / membrane protein / multi drug resistance / transporter
Function / homologyMulti antimicrobial extrusion protein / MatE / antiporter activity / xenobiotic transmembrane transporter activity / membrane => GO:0016020 / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / RUBIDIUM ION / Protein DETOXIFICATION
Function and homology information
Biological speciesCamelina sativa (false flax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsTanaka, Y. / Tsukazaki, T. / Iwaki, S.
CitationJournal: Structure / Year: 2017
Title: Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein
Authors: Tanaka, Y. / Iwaki, S. / Tsukazaki, T.
History
DepositionSep 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_database_related
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_database_related.content_type
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
A: multi drug efflux transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6676
Polymers51,4271
Non-polymers1,2415
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-23 kcal/mol
Surface area18670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.650, 69.240, 116.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein multi drug efflux transporter


Mass: 51426.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelina sativa (false flax) / Gene: false flax / Plasmid: pPic9k / Production host: Komagataella pastoris (fungus) / References: UniProt: R0G998*PLUS
#2: Chemical ChemComp-RB / RUBIDIUM ION / Rubidium


Mass: 85.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rb
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS USED THE NCBI Reference Sequence: XP_010514235.1.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 7.1
Details: 33% PEG300, 200mM (NH4)2SO4, 100mM Tris, 100mM RbCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: CCD / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45.623 Å / Num. obs: 21982 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 12.508 % / Biso Wilson estimate: 27.8 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.403 / Rrim(I) all: 0.418 / Χ2: 1.329 / Net I/σ(I): 6.48 / Num. measured all: 274945 / Scaling rejects: 227
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.4412.7252.4511.4235140.5542.54597.5
2.44-2.6112.5951.4322.1533100.7031.48798
2.61-2.8212.1770.982.9630560.8071.01996.8
2.82-3.0912.5390.6234.4528490.9060.64797.1
3.09-3.4512.8670.4156.6825530.9470.4398
3.45-3.9812.8470.26910.5222910.980.27997.7
3.98-4.8712.1440.21314.2819650.9820.22297.3
4.87-6.8911.8310.18613.3815430.9790.19496.1
6.89-45.62312.4330.11720.799010.9960.12294.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.65 Å45.63 Å
Translation6.65 Å45.63 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XSCALEdata scaling
PHASER2.5.3phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJJ

5xjj


Resolution: 2.3→45.623 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6
RfactorNum. reflection% reflection
Rfree0.2536 1999 9.12 %
Rwork0.2227 --
obs0.2256 21912 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.11 Å2 / Biso mean: 30.94 Å2 / Biso min: 14.55 Å2
Refinement stepCycle: final / Resolution: 2.3→45.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3453 0 77 84 3614
Biso mean--46.77 34.96 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023610
X-RAY DIFFRACTIONf_angle_d0.4444906
X-RAY DIFFRACTIONf_chiral_restr0.034583
X-RAY DIFFRACTIONf_plane_restr0.003594
X-RAY DIFFRACTIONf_dihedral_angle_d7.5612084
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3001-2.35760.32041390.2691391153097
2.3576-2.42140.25421410.25051404154598
2.4214-2.49260.28721410.23371397153897
2.4926-2.57310.24261410.22531410155198
2.5731-2.6650.29631410.21971404154598
2.665-2.77170.22081410.21151406154797
2.7717-2.89780.21741410.20561400154196
2.8978-3.05060.26791390.2231395153498
3.0506-3.24170.24721440.22221427157198
3.2417-3.49190.26611430.2171432157598
3.4919-3.84310.26111450.21231440158598
3.8431-4.39880.24641450.22241441158698
4.3988-5.54050.2471450.23481449159497
5.5405-45.63150.23891530.21181517167096

+
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