[English] 日本語
Yorodumi
- PDB-5xjj: Crystal structure of a MATE family protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xjj
TitleCrystal structure of a MATE family protein
Componentsmulti drug efflux transporter
KeywordsTRANSPORT PROTEIN / membrane protein / multidrug resistance / transporter
Function / homology
Function and homology information


cadmium ion transport / sequestering of metal ion / antiporter activity / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Multi antimicrobial extrusion protein / MatE
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Protein DETOXIFICATION
Similarity search - Component
Biological speciesCamelina sativa (false flax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTanaka, Y. / Tsukazaki, T. / Iwaki, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPS/MEXTJP26119007, JP26291023, JP16K14713, JP15H01537, JP15K06972 Japan
PRESTOJPMJPR12L3 Japan
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
DepositionMay 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: pdbx_database_related
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)49,9992
Polymers49,6431
Non-polymers3571
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19450 Å2
Unit cell
Length a, b, c (Å)60.710, 69.890, 117.600
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: 49642.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelina sativa (false flax) / Plasmid: pPic9k / Production host: Pichia pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: A0A2D0TCI5*PLUS
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 7.5 / Details: 30% PEG400, 100 mM NaCl, 100 mM Li2SO4

-
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: Nov 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.833 Å / Num. obs: 12420 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 5.331 % / Biso Wilson estimate: 40.15 Å2 / CC1/2: 0.929 / Rmerge(I) obs: 0.497 / Rrim(I) all: 0.544 / Χ2: 1.061 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.975.421.9871.2319850.3542.17997.9
2.97-3.175.4611.3751.5418510.5211.50497.9
3.17-3.435.3651.0162.1517810.6011.1196.7
3.43-3.765.1020.6583.1115910.7740.72295.2
3.76-4.25.3550.4694.7714210.8720.51295.5
4.2-4.855.5020.4116.0513100.860.4596.3
4.85-5.935.2960.3215.8911100.9310.35296.9
5.93-8.374.910.2246.598590.9620.24393.5
8.37-45.8335.3810.1659.655120.9790.17791.1

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata collection
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VVN

3vvn


Resolution: 2.9→45.833 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.56
RfactorNum. reflection% reflection
Rfree0.2956 1106 10.02 %
Rwork0.2387 --
obs0.2445 11035 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.52 Å2 / Biso mean: 35.9071 Å2 / Biso min: 6.77 Å2
Refinement stepCycle: final / Resolution: 2.9→45.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 25 10 3477
Biso mean--41.28 15.96 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033551
X-RAY DIFFRACTIONf_angle_d0.5414841
X-RAY DIFFRACTIONf_chiral_restr0.036578
X-RAY DIFFRACTIONf_plane_restr0.004589
X-RAY DIFFRACTIONf_dihedral_angle_d5.242039
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.0320.31751330.27761194132794
3.032-3.19190.30871390.27411222136195
3.1919-3.39180.31991350.25661218135396
3.3918-3.65360.32221350.26621223135896
3.6536-4.0210.32671380.24011237137595
4.021-4.60240.28621390.21971241138096
4.6024-5.79670.29281420.22821283142597
5.7967-45.83860.23751450.20631311145693
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8790.6845-4.91972.7284-0.57775.4936-0.28850.10940.34450.23580.358-0.14910.60140.11320.15560.3040.0077-0.12520.2259-0.03650.3006-6.571310.9532-2.792
20.818-0.4276-1.16570.3466-0.01764.5504-0.2938-0.0116-0.2933-0.0327-0.26120.0428-0.13970.0890.30130.2851-0.0118-0.00110.1591-0.04790.2983-13.5366-3.270.6076
31.3939-0.1329-0.09842.9258-0.58982.0793-0.09640.0534-0.04790.0694-0.00490.13220.0152-0.10470.08090.1575-0.0238-0.01650.22890.01270.1867-21.52231.5151-2.754
41.20530.64610.31842.0604-0.30863.093-0.3475-0.1681-0.0767-0.1496-0.3444-0.1058-0.02810.17780.51510.2528-0.0086-0.07110.2951-0.01070.3009-8.3901-9.2999-0.6643
51.10250.50641.40370.97280.60330.19350.202-0.1024-0.07730.2036-0.1222-0.1430.2217-0.3271-0.05550.339-0.02480.0880.30540.01350.25923.83275.80783.0778
63.3526-0.04070.1892.8754-0.164.7699-0.0591-0.6724-0.36580.1447-0.20420.02240.3055-0.13320.41830.2106-0.00310.02410.28250.07850.28776.6096-9.29126.0408
71.52291.2462-0.29391.29970.25080.85140.48980.918-0.3457-0.54770.1576-0.48440.8040.7057-0.11740.7494-0.07730.1910.6383-0.18920.43462.5076-8.6204-22.7799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 59 )A20 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 97 )A60 - 97
3X-RAY DIFFRACTION3chain 'A' and (resid 98 through 241 )A98 - 241
4X-RAY DIFFRACTION4chain 'A' and (resid 242 through 281 )A242 - 281
5X-RAY DIFFRACTION5chain 'A' and (resid 282 through 396 )A282 - 396
6X-RAY DIFFRACTION6chain 'A' and (resid 397 through 452 )A397 - 452
7X-RAY DIFFRACTION7chain 'A' and (resid 453 through 467 )A453 - 467

+
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