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- PDB-6jo0: Crystal structure of the DTS-motif rhodopsin from Phaeocystis glo... -

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Basic information

Entry
Database: PDB / ID: 6jo0
TitleCrystal structure of the DTS-motif rhodopsin from Phaeocystis globosa virus 12T
ComponentsVirRDTS
KeywordsMEMBRANE PROTEIN / microbial type rhodopsin from virus
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
DECANE / DODECANE / nonane / HEXANE / N-OCTANE / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / RETINAL / Uncharacterized protein
Similarity search - Component
Biological speciesPhaeocystis globosa virus 12T
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsHosaka, T. / Kimura-Someya, T. / Shirouzu, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators.
Authors: Needham, D.M. / Yoshizawa, S. / Hosaka, T. / Poirier, C. / Choi, C.J. / Hehenberger, E. / Irwin, N.A.T. / Wilken, S. / Yung, C.M. / Bachy, C. / Kurihara, R. / Nakajima, Y. / Kojima, K. / ...Authors: Needham, D.M. / Yoshizawa, S. / Hosaka, T. / Poirier, C. / Choi, C.J. / Hehenberger, E. / Irwin, N.A.T. / Wilken, S. / Yung, C.M. / Bachy, C. / Kurihara, R. / Nakajima, Y. / Kojima, K. / Kimura-Someya, T. / Leonard, G. / Malmstrom, R.R. / Mende, D.R. / Olson, D.K. / Sudo, Y. / Sudek, S. / Richards, T.A. / DeLong, E.F. / Keeling, P.J. / Santoro, A.E. / Shirouzu, M. / Iwasaki, W. / Worden, A.Z.
History
DepositionMar 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Structure summary
Category: citation_author / struct / Item: _citation_author.identifier_ORCID / _struct.title
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VirRDTS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,63720
Polymers28,0871
Non-polymers2,55019
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint21 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.194, 57.832, 117.037
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein VirRDTS


Mass: 28087.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeocystis globosa virus 12T / Gene: PGAG_00290 / Production host: Escherichia coli (E. coli) / References: UniProt: G8DI69

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Non-polymers , 9 types, 111 molecules

#2: Chemical ChemComp-RET / RETINAL / Retinal


Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14
#6: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#7: Chemical ChemComp-D12 / DODECANE / Dodecane


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#8: Chemical ChemComp-DD9 / nonane / Nonane


Mass: 128.255 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H20
#9: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


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


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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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: 2.79 Å3/Da / Density % sol: 55.87 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: Na-citrate (pH 5.5), 150 mM Na-phosphate, 25% PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→45.19 Å / Num. obs: 37658 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.686.61.62818190.6030.6781.76799
9.04-45.195.50.0462840.9960.0220.05198.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B2N

5b2n


Resolution: 1.651→42.16 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.83
RfactorNum. reflection% reflection
Rfree0.209 1855 4.94 %
Rwork0.1918 --
obs0.1926 37586 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.63 Å2 / Biso mean: 31.9584 Å2 / Biso min: 17.66 Å2
Refinement stepCycle: final / Resolution: 1.651→42.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 168 92 2212
Biso mean--47.77 40.52 -
Num. residues----224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6511-1.69570.30811510.30352679283099
1.6957-1.74560.32481590.279326902849100
1.7456-1.80190.32121240.260327152839100
1.8019-1.86640.25731480.240627142862100
1.8664-1.94110.21221430.200827032846100
1.9411-2.02940.19451190.180827332852100
2.0294-2.13640.18571260.165927542880100
2.1364-2.27030.19091610.158927202881100
2.2703-2.44550.17731530.155227322885100
2.4455-2.69160.17381440.154627422886100
2.6916-3.0810.17231350.170727902925100
3.081-3.88130.21151530.186628002953100
3.8813-42.17360.22151390.213429593098100
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)
12.28851.1419-0.33272.7919-2.00194.0041-0.06160.034-0.0449-0.7618-0.06070.15320.4072-0.03340.02710.20620.0127-0.02050.208-0.02720.14872.8776-30.7565-28.7905
21.441.43940.16622.2128-0.2261.7278-0.02010.09720.0752-0.03140.10740.1426-0.0814-0.0317-0.03970.2790.0011-0.01020.2496-0.00250.197511.5451-25.503-27.9713
31.29260.76840.32874.6194-0.2391.9880.06510.0431-0.12220.1719-0.02290.01790.09920.1029-0.03020.26050.0183-0.00180.2504-0.0020.168712.8217-31.8645-19.1714
40.8070.1454-0.15852.3425-1.55032.02050.0228-0.10980.08750.291-0.0863-0.2281-0.19490.09120.03950.3670.0074-0.0520.2618-0.02990.204518.4961-22.4905-10.5266
51.5487-0.69690.75522.6468-0.38212.4151-0.0435-0.13390.14460.20440.05490.2284-0.0966-0.2322-0.02150.25670.01630.02560.2537-0.00980.18884.4177-25.6586-14.9546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 34 )A3 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 63 )A35 - 63
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 101 )A64 - 101
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 167 )A102 - 167
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 225 )A168 - 225

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