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- PDB-4hyj: Crystal structure of Exiguobacterium sibiricum rhodopsin -

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Basic information

Entry
Database: PDB / ID: 4hyj
TitleCrystal structure of Exiguobacterium sibiricum rhodopsin
ComponentsRhodopsin
KeywordsPROTON TRANSPORT / Seven-helical transmembrane protein / Proton pump / Membrane
Function / homology
Function and homology information


light-activated monoatomic ion channel activity / : / photoreceptor activity / phototransduction / membrane => GO:0016020
Similarity search - Function
Proteorhodopsin / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / 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
EICOSANE / RETINAL / Rhodopsin
Similarity search - Component
Biological speciesExiguobacterium sibiricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGushchin, I. / Chervakov, P. / Kuzmichev, P. / Popov, A. / Round, E. / Borshchevskiy, V. / Dolgikh, D. / Kirpichnikov, M. / Petrovskaya, L. / Chupin, V. ...Gushchin, I. / Chervakov, P. / Kuzmichev, P. / Popov, A. / Round, E. / Borshchevskiy, V. / Dolgikh, D. / Kirpichnikov, M. / Petrovskaya, L. / Chupin, V. / Arseniev, A. / Gordeliy, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria.
Authors: Gushchin, I. / Chervakov, P. / Kuzmichev, P. / Popov, A.N. / Round, E. / Borshchevskiy, V. / Ishchenko, A. / Petrovskaya, L. / Chupin, V. / Dolgikh, D.A. / Arseniev, A.A. / Kirpichnikov, M. / Gordeliy, V.
History
DepositionNov 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhodopsin
B: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,30934
Polymers57,2642
Non-polymers9,04532
Water59433
1
A: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,30714
Polymers28,6321
Non-polymers3,67513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Rhodopsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,00220
Polymers28,6321
Non-polymers5,37019
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.099, 96.099, 124.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Rhodopsin


Mass: 28631.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sibiricum (bacteria) / Gene: Exig_1419 / Production host: Escherichia coli (E. coli) / References: UniProt: B1YFV8
#2: Chemical ChemComp-RET / RETINAL


Mass: 284.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O
#3: Chemical...
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C20H42
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 295 K / Method: cubic phase crystallization / Details: Cubic phase crystallization, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.15→69.17 Å / Num. all: 36642 / Num. obs: 35982 / % possible obs: 98 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.7 / % possible all: 96.7

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model based on PDB ENTRY 3DDL

3ddl


Resolution: 2.3→69.169 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 1498 5.09 %RANDOM
Rwork0.1754 ---
obs0.1775 29408 97.65 %-
all-30116 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→69.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 343 33 3870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083909
X-RAY DIFFRACTIONf_angle_d1.4015213
X-RAY DIFFRACTIONf_dihedral_angle_d16.2241430
X-RAY DIFFRACTIONf_chiral_restr0.165595
X-RAY DIFFRACTIONf_plane_restr0.005601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.37430.23121320.18452408X-RAY DIFFRACTION94
2.3743-2.45910.21431240.17142583X-RAY DIFFRACTION100
2.4591-2.55760.21711160.16132557X-RAY DIFFRACTION100
2.5576-2.6740.25671430.15612566X-RAY DIFFRACTION100
2.674-2.8150.22571370.15752485X-RAY DIFFRACTION98
2.815-2.99140.20041310.15712447X-RAY DIFFRACTION95
2.9914-3.22230.23391430.16362569X-RAY DIFFRACTION99
3.2223-3.54660.20861250.17072576X-RAY DIFFRACTION99
3.5466-4.05980.19781540.16412465X-RAY DIFFRACTION95
4.0598-5.11460.17061770.16382593X-RAY DIFFRACTION100
5.1146-69.19980.30921160.22312661X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -23.6429 Å / Origin y: -42.7611 Å / Origin z: -32.3769 Å
111213212223313233
T0.0727 Å20.0224 Å20.0196 Å2-0.1179 Å20.0191 Å2--0.0941 Å2
L0.7782 °20.0667 °2-0.0488 °2-0.4373 °20.3516 °2--0.7056 °2
S0.0026 Å °-0.109 Å °0.0322 Å °-0.0285 Å °-0.0583 Å °-0.0115 Å °0.0511 Å °0.0058 Å °-0.0009 Å °
Refinement TLS groupSelection details: all

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