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- PDB-6eyu: Crystal structure of the inward H(+) pump xenorhodopsin -

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Basic information

Entry
Database: PDB / ID: 6eyu
TitleCrystal structure of the inward H(+) pump xenorhodopsin
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / Retinal protein / proton transport
Function / homologyBacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / EICOSANE / Chem-MUN / RETINAL / Bacteriorhodopsin
Function and homology information
Biological speciesNanosalina sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKovalev, K. / Shevchenko, V. / Polovinkin, V. / Mager, T. / Gushchin, I. / Melnikov, I. / Borshchevskiy, V. / Popov, A. / Alekseev, A. / Gordeliy, V.
Funding support France, Germany, Russian Federation, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0029-02 France
German Research FoundationANR-15-CE11-0029-02 Germany
French Infrastructure for Integrated Structural BiologyANR-10-INSB-05-02 France
GRAANR-10-LABX-49-01 France
ERA.Net RUS PLUS and Ministry of Education and Science of the Russian FederationID 323, RFMEFI58715X0011 Russian Federation
CitationJournal: Sci Adv / Year: 2017
Title: Inward H(+) pump xenorhodopsin: Mechanism and alternative optogenetic approach.
Authors: Shevchenko, V. / Mager, T. / Kovalev, K. / Polovinkin, V. / Alekseev, A. / Juettner, J. / Chizhov, I. / Bamann, C. / Vavourakis, C. / Ghai, R. / Gushchin, I. / Borshchevskiy, V. / Rogachev, ...Authors: Shevchenko, V. / Mager, T. / Kovalev, K. / Polovinkin, V. / Alekseev, A. / Juettner, J. / Chizhov, I. / Bamann, C. / Vavourakis, C. / Ghai, R. / Gushchin, I. / Borshchevskiy, V. / Rogachev, A. / Melnikov, I. / Popov, A. / Balandin, T. / Rodriguez-Valera, F. / Manstein, D.J. / Bueldt, G. / Bamberg, E. / Gordeliy, V.
History
DepositionNov 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Structure summary
Category: audit_author / pdbx_audit_support ...audit_author / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _audit_author.identifier_ORCID / _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriorhodopsin
B: Bacteriorhodopsin
C: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,51544
Polymers77,5543
Non-polymers10,96141
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Trimeric form
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14230 Å2
ΔGint-34 kcal/mol
Surface area24210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.010, 93.870, 196.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bacteriorhodopsin / Inward H(+) pump xenorhodopsin (NsXeR)


Mass: 25851.322 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanosalina sp. (strain J07AB43) (archaea)
Strain: J07AB43 / Gene: J07AB43_12860 / Production host: Escherichia coli (E. coli) / References: UniProt: G0QG75
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H42
#4: Chemical...
ChemComp-MUN / [(2~{S})-2,3-bis(oxidanyl)propyl] (~{E})-undec-2-enoate / MONOUNDECENOIN


Mass: 258.354 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C14H26O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
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: 3.82 Å3/Da / Density % sol: 67.82 %
Crystal growTemperature: 295 K / Method: lipidic cubic phase
Details: 1:1 protein-solution-to-monoundecenoin ratio; protein concentration of 30mg/ml; 2.8 - 3.4 M sodium malonate; pH 8.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.969 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.5→12 Å / Num. obs: 41796 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 21.562 % / Biso Wilson estimate: 60.793 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.286 / Rrim(I) all: 0.293 / Χ2: 0.995 / Net I/σ(I): 9.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.5617.7591.8590.9830620.3291.91499.9
2.56-2.6418.9481.6571.1729550.331.702100
2.64-2.7119.5751.4791.4628910.3641.518100
2.71-2.819.6141.3261.7928060.3871.36100
2.8-2.8920.6211.222.2827090.5321.251100
2.89-2.9922.671.1352.6726390.6571.161100
2.99-3.122.5950.9963.3325510.7281.019100
3.1-3.2322.730.9224.0424700.7960.943100
3.23-3.3722.1160.7695.0723760.8750.787100
3.37-3.5421.8130.6246.922460.9320.639100
3.54-3.7323.0810.5069.2721420.9710.517100
3.73-3.9523.5150.38113.3220630.9870.389100
3.95-4.2323.4130.29417.7919260.9920.301100
4.23-4.5622.5570.2423.6518080.9960.245100
4.56-523.3920.25825.1716560.9970.26499.9
5-5.5924.1080.24423.2715210.9970.25100
5.59-6.4523.5820.20521.4113540.9970.209100
6.45-7.9122.40.11528.1611670.9990.118100
7.91-11.1822.3340.06240.4591210.064100
11.18-1219.450.05745.465420.9990.05998.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XIO

1xio


Resolution: 2.5→12 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 33.406 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.339 / ESU R Free: 0.254
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2069 5 %RANDOM
Rwork0.2097 ---
obs0.2119 39282 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 164.18 Å2 / Biso mean: 74.755 Å2 / Biso min: 47.33 Å2
Baniso -1Baniso -2Baniso -3
1-4.55 Å2-0 Å2-0 Å2
2--7.02 Å2-0 Å2
3----11.57 Å2
Refinement stepCycle: final / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5448 0 545 53 6046
Biso mean--104.14 97.2 -
Num. residues----693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.026117
X-RAY DIFFRACTIONr_bond_other_d0.0040.0216077
X-RAY DIFFRACTIONr_angle_refined_deg0.4272.0348192
X-RAY DIFFRACTIONr_angle_other_deg0.6543.02713861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7585690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17523.134201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.47515816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.839159
X-RAY DIFFRACTIONr_chiral_restr0.0330.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0260.0216312
X-RAY DIFFRACTIONr_gen_planes_other0.0340.021276
LS refinement shellResolution: 2.5→2.562 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 147 -
Rwork0.383 2784 -
all-2931 -
obs--99.76 %
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)
11.11360.05480.56610.75460.01741.6161-0.0480.0534-0.018-0.00480.0002-0.00960.05870.0860.04770.1106-0.0085-0.00530.00690.030.9654-1.4444-24.496528.1438
20.48180.1015-0.0580.28120.36161.3641-0.0166-0.07010.0352-0.0479-0.06580.0462-0.0375-0.18030.08240.0928-0.0013-0.00370.0842-0.02610.9406-28.904-12.471925.7909
30.8299-0.1660.07870.7390.16821.2027-0.02990.04140.0049-0.17130.01260.0077-0.05950.06960.01730.1904-0.02470.00640.008-0.00770.9353-4.47145.269324.8447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 232
2X-RAY DIFFRACTION2B1 - 232
3X-RAY DIFFRACTION3C1 - 229

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