[English] 日本語
Yorodumi
- PDB-6kfq: Crystal structure of thermophilic rhodopsin from Rubrobacter xyla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kfq
TitleCrystal structure of thermophilic rhodopsin from Rubrobacter xylanophilus
ComponentsRhodopsin
KeywordsTRANSPORT PROTEIN / Rhodopsin / Transporter / H+ transport
Function / homology
Function and homology information


: / photoreceptor activity / phototransduction / monoatomic ion channel activity / membrane => GO:0016020
Similarity search - Function
Bacterial rhodopsins retinal binding site. / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MPG / RETINAL / Rhodopsin
Similarity search - Component
Biological speciesRubrobacter xylanophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsSuzuki, K. / Akiyama, T. / Hayashi, T. / Yasuda, S. / Kanehara, K. / Kojima, K. / Tanabe, M. / Kato, R. / Senda, T. / Sudo, Y. ...Suzuki, K. / Akiyama, T. / Hayashi, T. / Yasuda, S. / Kanehara, K. / Kojima, K. / Tanabe, M. / Kato, R. / Senda, T. / Sudo, Y. / Kinoshita, M. / Murata, T.
CitationJournal: J.Phys.Chem.B / Year: 2020
Title: How Does a Microbial Rhodopsin RxR Realize Its Exceptionally High Thermostability with the Proton-Pumping Function Being Retained?
Authors: Hayashi, T. / Yasuda, S. / Suzuki, K. / Akiyama, T. / Kanehara, K. / Kojima, K. / Tanabe, M. / Kato, R. / Senda, T. / Sudo, Y. / Murata, T. / Kinoshita, M.
History
DepositionJul 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,02920
Polymers25,8481
Non-polymers6,18119
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-15 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.930, 68.410, 107.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

#1: Protein Rhodopsin


Mass: 25847.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubrobacter xylanophilus (strain DSM 9941 / NBRC 16129) (bacteria)
Strain: DSM 9941 / NBRC 16129 / Gene: Rxyl_2037 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1AUE6
#2: Chemical
ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 296 K / Method: lipidic cubic phase / pH: 6
Details: 100 mM MES (pH 6.0), 100 mM Li2SO4, 30% PEG 600 (v/v)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→42.37 Å / Num. obs: 19923 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.74 Å2 / CC1/2: 1 / Rrim(I) all: 0.072 / Net I/σ(I): 17.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
5.48-42.375.6953.2385810.02199.1
3.89-5.486.2155.2414110.9990.02899.8
2.76-3.186.3838.4317920.9990.04299.8
2.47-2.766.4323.9420650.9970.078100
2.25-2.476.5216.1723490.9960.11999.9
2.09-2.256.579.825850.9890.19699.9
1.95-2.096.626.4527810.9740.299100
1.95-2.096.663.6229870.940.52100
1.84-1.956.361.8731590.8270.96198

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y9H

4y9h


Resolution: 1.84→34.2 Å / SU ML: 0.2217 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.6633
RfactorNum. reflection% reflection
Rfree0.2265 997 5.01 %
Rwork0.1925 --
obs0.1942 19905 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.98 Å2
Refinement stepCycle: LAST / Resolution: 1.84→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 218 20 1982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491992
X-RAY DIFFRACTIONf_angle_d0.7352655
X-RAY DIFFRACTIONf_chiral_restr0.0408313
X-RAY DIFFRACTIONf_plane_restr0.0049297
X-RAY DIFFRACTIONf_dihedral_angle_d14.09011157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.940.34661370.27822586X-RAY DIFFRACTION97.63
1.94-2.060.27941400.22232657X-RAY DIFFRACTION99.75
2.06-2.220.23721400.19462667X-RAY DIFFRACTION100
2.22-2.440.23791420.18242683X-RAY DIFFRACTION99.89
2.44-2.790.21971420.17982706X-RAY DIFFRACTION99.86
2.79-3.520.21511440.1882731X-RAY DIFFRACTION99.93
3.52-34.20.21041520.18812878X-RAY DIFFRACTION99.57
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)
11.85685338582-0.140702775388-0.7987987772631.907840861310.3577545027591.19118862031-0.07014124916580.068661419335-0.09939840374670.678345149281-0.1499785759550.3076393696110.764013199986-0.4371577519830.1807930888480.5035295858-0.1749081995580.1398769068790.282930369784-0.1000792959390.3812345333757.94587052537-19.5665835148-24.8095253181
21.46751648544-0.335453982646-0.8699180699541.881051830541.062410474663.072236963360.0719726725902-0.114098412512-0.04707031696080.472389166072-0.4753030758660.5374887934520.175224873223-0.7907996802680.2508505704080.315314020802-0.1991730867370.1122638310620.458948175237-0.1641599958580.3949857795322.8333698616-12.3882904313-22.6022988004
30.597666371381-0.1741524989690.9050921795242.884247418660.561671522134.81105353467-0.05683413723180.219339855877-0.0345365048921-0.444955489706-0.3225120171880.281159012715-0.026895273972-0.6419541354870.3440129486740.1742579518980.0421385540972-0.03274198488360.313693024808-0.06195878905430.2600339601036.65156451059-3.26735755173-28.0495028432
46.07886022208-1.825263665173.137341530714.09431064634-1.196184270361.64154852131-0.521230603282-0.676061589035-0.2609671102362.01762643497-0.01222877074581.64277479932-0.214838063863-1.105219302270.5700700072260.8920585514030.1256771667870.2210988012810.535990121998-0.03159759558280.5445717575771.926218034522.85979261374-3.49434839955
52.02619432115-0.9618784553440.2750111721764.50495319360.4982789363324.263218335020.1082504817660.1443822447190.194997333531-0.342801347805-0.137167989146-0.187170549028-0.595784484597-0.2443619874270.001855180943910.281723353080.0959689961818-0.02570304740660.204933454125-0.008527593765910.28872889406110.17812184886.81185347558-22.452512152
61.58673275956-0.641382022158-1.626029483723.81901997263-0.5530265031378.21620837235-0.118357676185-0.1882254976360.02004438463120.4372682017810.0208295985359-0.3625946519010.09457650581810.3771823878620.02827670979970.1964916738910.00900852451822-0.03621230633480.178168529913-0.01782116142710.24744747990716.9308905999-3.55955595134-16.598812754
71.25717596199-0.792382052547-0.3398678979333.653271462922.581495705782.827711272280.05176165325860.1482455979170.0142139659167-0.127988308941-0.0722543159119-0.1346578573220.0550368803572-0.1251405695790.00261686500380.176034806854-0.005774210738280.02234060784970.219115976309-0.01552404450550.30603880161415.7880595108-9.17012272295-28.9330354893
85.431247393010.331713132173-0.1103569563465.717028473153.653319629572.353374823390.0420492942342-0.61850743413-0.4889361487770.82440644052-0.4619789162790.1151766987230.916102019271-0.1294296581020.4213759195141.09610642467-0.08549391332210.168211780910.3413480292780.01182923523320.3424900570128.02690044062-12.9334464713-1.08292252373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 97 )
5X-RAY DIFFRACTION5chain 'A' and (resid 98 through 155 )
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 184 )
7X-RAY DIFFRACTION7chain 'A' and (resid 185 through 217 )
8X-RAY DIFFRACTION8chain 'A' and (resid 218 through 229 )

+
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