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- PDB-3ddl: Crystallographic Structure of Xanthorhodopsin, a Light-Driven Ion... -

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Basic information

Entry
Database: PDB / ID: 3ddl
TitleCrystallographic Structure of Xanthorhodopsin, a Light-Driven Ion Pump with Dual Chromophore
ComponentsXanthorhodopsin
KeywordsTRANSPORT PROTEIN / rhodopsin / carotenoid / ion pump / light-harvesting / antenna / retinal
Function / homology
Function and homology information


light-activated monoatomic ion channel activity / photoreceptor activity / phototransduction / membrane
Similarity search - Function
Proteorhodopsin / 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
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / RETINAL / Salinixanthin / Unknown ligand / Xanthorhodopsin
Similarity search - Component
Biological speciesSalinibacter ruber (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsStagno, J. / Luecke, H. / Schobert, B. / Lanyi, J.K. / Imasheva, E.S. / Wang, J.M. / Balashov, S.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore.
Authors: Luecke, H. / Schobert, B. / Stagno, J. / Imasheva, E.S. / Wang, J.M. / Balashov, S.P. / Lanyi, J.K.
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 8, 2016Group: Atomic model
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xanthorhodopsin
B: Xanthorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,18429
Polymers60,2102
Non-polymers3,97427
Water1,11762
1
A: Xanthorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,35911
Polymers30,1051
Non-polymers1,25410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xanthorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,82518
Polymers30,1051
Non-polymers2,72017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.740, 59.490, 59.720
Angle α, β, γ (deg.)76.35, 74.93, 64.08
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Xanthorhodopsin


Mass: 30105.006 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Salinibacter ruber (bacteria) / References: UniProt: Q2S2F8

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Non-polymers , 6 types, 89 molecules

#2: Chemical ChemComp-SXN / Salinixanthin / (3'E)-2'-hydroxy-4-oxo-3',4'-didehydro-1',2'-dihydro-beta,psi-caroten-1'-yl 6-O-(13-methyltetradecanoyl)-alpha-L-idopyranoside


Mass: 969.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C61H92O9
#3: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 21 / Source method: obtained synthetically
#4: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#5: Chemical ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#6: Chemical ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE HETERO GROUPS UNL 402-409 CHAIN A AND UNL 402-414 CHAIN B ARE CARBON CHAINS THAT REPRESENT ...THE HETERO GROUPS UNL 402-409 CHAIN A AND UNL 402-414 CHAIN B ARE CARBON CHAINS THAT REPRESENT FATTY ACID CHAINS OF PHOSPHOLIPIDS INTERACTING WITH THE PROTEIN. AS THE ELECTRON DENSITY WAS NOT CLEAR ENOUGH TO SUPPORT THE ENTIRE PHOSPHOLIPID IN EACH CASE, THE ACTUAL IDENTITY OF EACH UNL HETERO GROUP IS UNKNOWN. ELECTRON DENSITY WAS NOT CLEAR ENOUGH TO DETERMINE WHETHER THE FATTY ACID CHAIN IS UNSATURATED. THEREFORE, ALL C-C BONDS FOR PCW HETERO GROUP WERE REFINED AS SINGLE BONDS.

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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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 5mg/ml xanthorhodopsin in 30mM phosphate pH 5.6, 1mM Na azide was solubilized in 1/3 volume of 16.7% dimyristoyl phoshatidylcholine in 20% nonyl maltoside. Crystals grew in 2.5-3M Na ...Details: 5mg/ml xanthorhodopsin in 30mM phosphate pH 5.6, 1mM Na azide was solubilized in 1/3 volume of 16.7% dimyristoyl phoshatidylcholine in 20% nonyl maltoside. Crystals grew in 2.5-3M Na phosphate, pH 5.6, 2.5 mM Na azide after 3-4 months, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→45.1 Å / Num. obs: 46289 / % possible obs: 94.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Χ2: 0.99 / Net I/σ(I): 8.4 / Scaling rejects: 1260
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.9-1.973.530.4851.51501242151.3585.5
1.97-2.053.570.3632.21685846711.394.9
2.05-2.143.580.2872.61696147011.2195
2.14-2.253.580.2153.81670746311.1995.6
2.25-2.393.570.155.11714247681.0495.1
2.39-2.583.590.1116.51690146820.9496.2
2.58-2.843.620.0779.31721047360.8295.8
2.84-3.253.630.05712.71713746950.7495.7
3.25-4.093.630.04817.11694446390.6994.4
4.09-45.13.680.03721.91694845510.792.5

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Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
d*TREKdata reduction
PHASERphasing
RefinementResolution: 1.9→45.1 Å / FOM work R set: 0.712 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.265 2333 4.7 %
Rwork0.247 --
obs-46278 94.1 %
Solvent computationBsol: 97.153 Å2
Displacement parametersBiso mean: 46.446 Å2
Baniso -1Baniso -2Baniso -3
1-16.933 Å23.302 Å2-16.013 Å2
2---0.766 Å2-6.765 Å2
3----16.167 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3925 0 430 62 4417
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.349
X-RAY DIFFRACTIONc_mcbond_it1.4131.5
X-RAY DIFFRACTIONc_scbond_it1.9732
X-RAY DIFFRACTIONc_mcangle_it2.2572
X-RAY DIFFRACTIONc_scangle_it2.8592.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dmp.pardmp.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4lip.parlip.top
X-RAY DIFFRACTION5sxn.parsxn.top

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