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- PDB-8anq: Crystal structure of the microbial rhodopsin from Sphingomonas pa... -

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Basic information

Entry
Database: PDB / ID: 8anq
TitleCrystal structure of the microbial rhodopsin from Sphingomonas paucimobilis (SpaR)
ComponentsBacteriorhodopsin
KeywordsMEMBRANE PROTEIN / rhodopsin / retinal / photocycle / proton transport / ion transport / microbial rhodopsins
Function / homology
Function and homology information


photoreceptor activity / phototransduction / monoatomic ion channel activity / 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
EICOSANE / Bacteriorhodopsin
Similarity search - Component
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKovalev, K. / Okhrimenko, I. / Marin, E. / Gordeliy, V.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Chem / Year: 2023
Title: Mirror proteorhodopsins.
Authors: Okhrimenko, I.S. / Kovalev, K. / Petrovskaya, L.E. / Ilyinsky, N.S. / Alekseev, A.A. / Marin, E. / Rokitskaya, T.I. / Antonenko, Y.N. / Siletsky, S.A. / Popov, P.A. / Zagryadskaya, Y.A. / ...Authors: Okhrimenko, I.S. / Kovalev, K. / Petrovskaya, L.E. / Ilyinsky, N.S. / Alekseev, A.A. / Marin, E. / Rokitskaya, T.I. / Antonenko, Y.N. / Siletsky, S.A. / Popov, P.A. / Zagryadskaya, Y.A. / Soloviov, D.V. / Chizhov, I.V. / Zabelskii, D.V. / Ryzhykau, Y.L. / Vlasov, A.V. / Kuklin, A.I. / Bogorodskiy, A.O. / Mikhailov, A.E. / Sidorov, D.V. / Bukhalovich, S. / Tsybrov, F. / Bukhdruker, S. / Vlasova, A.D. / Borshchevskiy, V.I. / Dolgikh, D.A. / Kirpichnikov, M.P. / Bamberg, E. / Gordeliy, V.I.
History
DepositionAug 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Bacteriorhodopsin
C: Bacteriorhodopsin
A: Bacteriorhodopsin
P: Bacteriorhodopsin
T: Bacteriorhodopsin
Y: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,07218
Polymers159,6816
Non-polymers3,39112
Water59433
1
B: Bacteriorhodopsin
C: Bacteriorhodopsin
A: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5369
Polymers79,8413
Non-polymers1,6956
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: Bacteriorhodopsin
T: Bacteriorhodopsin
Y: Bacteriorhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5369
Polymers79,8413
Non-polymers1,6956
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)233.339, 65.027, 124.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12B
22A
13B
23P
14B
24T
15B
25Y
16C
26A
17C
27P
18C
28T
19C
29Y
110A
210P
111A
211T
112A
212Y
113P
213T
114P
214Y
115T
215Y

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISBA2 - 2292 - 229
21HISHISCB2 - 2282 - 228
12ARGARGBA2 - 2272 - 227
22ARGARGAC2 - 2272 - 227
13HISHISBA2 - 2292 - 229
23HISHISPD2 - 2292 - 229
14HISHISBA2 - 2292 - 229
24HISHISTE2 - 2282 - 228
15HISHISBA2 - 2282 - 228
25HISHISYF2 - 2282 - 228
16ARGARGCB2 - 2272 - 227
26ARGARGAC2 - 2272 - 227
17HISHISCB2 - 2282 - 228
27HISHISPD2 - 2292 - 229
18HISHISCB2 - 2282 - 228
28HISHISTE2 - 2282 - 228
19HISHISCB2 - 2282 - 228
29HISHISYF2 - 2282 - 228
110ARGARGAC2 - 2272 - 227
210ARGARGPD2 - 2272 - 227
111ARGARGAC2 - 2272 - 227
211ARGARGTE2 - 2272 - 227
112LEULEUAC2 - 2262 - 226
212LEULEUYF2 - 2262 - 226
113HISHISPD2 - 2292 - 229
213HISHISTE2 - 2282 - 228
114HISHISPD2 - 2282 - 228
214HISHISYF2 - 2282 - 228
115HISHISTE2 - 2282 - 228
215HISHISYF2 - 2282 - 228

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Bacteriorhodopsin


Mass: 26613.523 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Gene: HKX06_19670, I6G38_01705 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A411LJN5
#2: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H42
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 1.6M Ammonium Phosphate pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975997 Å / Relative weight: 1
ReflectionResolution: 2.8→46.32 Å / Num. obs: 44606 / % possible obs: 96.4 % / Redundancy: 2.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.133 / Rrim(I) all: 0.218 / Net I/σ(I): 4.6 / Num. measured all: 104259 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.912.31.2451059547020.3960.981.5920.797.3
10.48-46.322.20.021190086510.0180.0282091.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1c3w

1c3w


Resolution: 2.8→19.91 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.888 / SU B: 29.332 / SU ML: 0.498 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 9.616 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3033 2215 5 %RANDOM
Rwork0.2746 ---
obs0.2761 42268 95.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.76 Å2 / Biso mean: 52.68 Å2 / Biso min: 20.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å20.36 Å2
2--4.93 Å20 Å2
3----4.44 Å2
Refinement stepCycle: final / Resolution: 2.8→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10354 0 162 33 10549
Biso mean--60.62 47.29 -
Num. residues----1359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01310802
X-RAY DIFFRACTIONr_bond_other_d00.01610839
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.61914783
X-RAY DIFFRACTIONr_angle_other_deg1.0371.54924704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.16851351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06419.503362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.943151449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.9011523
X-RAY DIFFRACTIONr_chiral_restr0.0290.21463
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211752
X-RAY DIFFRACTIONr_gen_planes_other00.022414
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B72000.11
12C72000.11
21B71560.11
22A71560.11
31B76650.02
32P76650.02
41B71870.11
42T71870.11
51B71620.11
52Y71620.11
61C72150.1
62A72150.1
71C71960.11
72P71960.11
81C76610.03
82T76610.03
91C72160.1
92Y72160.1
101A71540.11
102P71540.11
111A72020.1
112T72020.1
121A76030.03
122Y76030.03
131P71820.11
132T71820.11
141P71550.11
142Y71550.11
151T72110.1
152Y72110.1
LS refinement shellResolution: 2.8→2.871 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 149 -
Rwork0.397 3083 -
all-3232 -
obs--96.56 %

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