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- PDB-6kfq: Crystal structure of thermophilic rhodopsin from Rubrobacter xyla... -

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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


monoatomic ion channel activity / photoreceptor activity / phototransduction / membrane
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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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)

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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

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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 )

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