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- PDB-6lm1: The crystal structure of cyanorhodopsin (CyR) N4075R from cyanoba... -

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Basic information

Entry
Database: PDB / ID: 6lm1
TitleThe crystal structure of cyanorhodopsin (CyR) N4075R from cyanobacteria Tolypothrix sp. NIES-4075
ComponentsRhodopsin
KeywordsMEMBRANE PROTEIN / Bacterial type rhodopsin RETINAL CELL-FREE SYNTHESIS / Cyanobacteria
Function / homology
Function and homology information


monoatomic ion channel activity / photoreceptor activity / phototransduction / metal ion binding / membrane
Similarity search - Function
Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
TETRADECANE / DECANE / DODECANE / HEXANE / NITRATE ION / N-OCTANE / HEXADECANE / RETINAL / Rhodopsin
Similarity search - Component
Biological speciesTolypothrix sp. NIES-4075 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHosaka, T. / Kimura-Someya, T. / Shirouzu, M.
CitationJournal: Sci Rep / Year: 2020
Title: A unique clade of light-driven proton-pumping rhodopsins evolved in the cyanobacterial lineage.
Authors: Hasegawa, M. / Hosaka, T. / Kojima, K. / Nishimura, Y. / Nakajima, Y. / Kimura-Someya, T. / Shirouzu, M. / Sudo, Y. / Yoshizawa, S.
History
DepositionDec 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 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 1.2Nov 6, 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
B: Rhodopsin
C: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,92372
Polymers84,7543
Non-polymers9,16869
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.920, 129.666, 127.626
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Rhodopsin


Mass: 28251.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tolypothrix sp. NIES-4075 (bacteria) / Gene: NIES4075_41530 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A218QMM7

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Non-polymers , 10 types, 258 molecules

#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C6H14 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C8H18 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C14H30 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.69 Å3/Da / Density % sol: 54.19 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1M sodium-acetate (pH5.0), 450mM Magnesium nitrate, 28% PEG 500

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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: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→49.7 Å / Num. obs: 129542 / % possible obs: 82.6 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.038 / Rrim(I) all: 0.13 / Net I/σ(I): 10 / Num. measured all: 1396532 / Scaling rejects: 55
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible allNet I/σ(I) obs
1.45-1.481.90.3897414387650.0010.3773854.34510
7.95-49.713.50.0371442910700.9990.0110.03999.652

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C3W

1c3w


Resolution: 1.9→45.479 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2041 1090 1.54 %
Rwork0.1653 69466 -
obs0.1658 70556 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.11 Å2 / Biso mean: 36.8638 Å2 / Biso min: 15.58 Å2
Refinement stepCycle: final / Resolution: 1.9→45.479 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5207 0 641 189 6037
Biso mean--52.24 50.17 -
Num. residues----678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9-1.98650.21191350.1878605
1.9865-2.09120.17681340.15938607
2.0912-2.22220.18271360.14738618
2.2222-2.39380.15971360.13528626
2.3938-2.63470.17221360.13878660
2.6347-3.01590.16551350.14478675
3.0159-3.79940.20061370.17188720
3.7994-45.4790.25461410.18768955
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)
12.9593-1.03610.2152.82720.01652.06880.04330.0984-0.11490.0691-0.0156-0.0725-0.00110.0766-0.01640.16430.0156-0.00620.2233-0.03890.180380.025233.280259.8708
20.99870.12560.62081.6516-0.87171.60730.1058-0.19880.00160.0914-0.0850.058-0.08390.0239-0.00680.2142-0.0054-0.00840.18130.00340.180368.069436.204173.988
31.78760.67390.24722.72531.27071.23230.08250.03550.03330.0849-0.0285-0.0943-0.00950.0448-0.04520.20940.0226-0.03170.18020.00180.183666.666741.713462.1695
42.89250.51570.22014.3169-0.17293.6854-0.0798-0.17140.10410.19980.0011-0.0509-0.2347-0.90330.11490.1690.0319-0.00590.53930.01420.254162.096936.921392.9255
52.33530.81721.0692.11841.49043.37310.0851-0.2229-0.1323-0.05040.11840.03040.0625-0.3445-0.11680.2687-0.0221-0.00920.3750.05380.233469.832331.177789.6006
61.2688-0.3092-0.57011.12380.08281.57020.0809-0.01510.11080.1062-0.0897-0.0353-0.1548-0.0209-0.00160.22410.01080.00990.26490.02170.208884.329136.380894.3587
72.66770.85330.13932.2009-0.13693.21250.062-0.17740.1844-0.143-0.0390.134-0.3031-0.4122-0.01940.25730.06090.03180.3262-0.00790.175374.914342.4213101.4956
82.65030.78610.12042.1046-1.27422.785-0.0533-0.18110.0070.03710.00340.1092-0.0967-0.00030.08640.16370.02780.00130.25840.04330.1608100.344733.645887.4384
91.67110.46640.07981.30830.47030.68380.02580.07170.0079-0.1213-0.10750.0351-0.1089-0.12920.08210.18910.0146-0.01020.19930.01080.209493.859535.94670.019
101.8609-0.5816-0.21342.49380.12181.5139-0.0208-0.14860.0932-0.02330.02110.0929-0.18840.04310.01210.1873-0.01510.0050.19420.01370.2246104.785641.712274.4123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 71 )A0 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 144 )A72 - 144
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 227 )A145 - 227
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 35 )B0 - 35
5X-RAY DIFFRACTION5chain 'B' and (resid 36 through 71 )B36 - 71
6X-RAY DIFFRACTION6chain 'B' and (resid 72 through 144 )B72 - 144
7X-RAY DIFFRACTION7chain 'B' and (resid 145 through 227 )B145 - 227
8X-RAY DIFFRACTION8chain 'C' and (resid 0 through 71 )C0 - 71
9X-RAY DIFFRACTION9chain 'C' and (resid 72 through 144 )C72 - 144
10X-RAY DIFFRACTION10chain 'C' and (resid 145 through 227 )C145 - 227

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