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- PDB-6nwd: X-ray Crystallographic structure of Gloeobacter rhodopsin -

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Basic information

Entry
Database: PDB / ID: 6nwd
TitleX-ray Crystallographic structure of Gloeobacter rhodopsin
ComponentsGll0198 protein
KeywordsTRANSPORT PROTEIN / Proton pump / Photoreceptor
Function / homology
Function and homology information


light-activated monoatomic ion channel activity / : / photoreceptor activity / phototransduction / membrane => GO:0016020 / identical protein binding
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
DECANE / DODECANE / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / RETINAL / Gll0198 protein
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsErnst, O.P. / Morizumi, T. / Ou, W.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other governmentCanada Excellence Research Chair Canada
CitationJournal: Sci Rep / Year: 2019
Title: X-ray Crystallographic Structure and Oligomerization of Gloeobacter Rhodopsin.
Authors: Morizumi, T. / Ou, W.L. / Van Eps, N. / Inoue, K. / Kandori, H. / Brown, L.S. / Ernst, O.P.
History
DepositionFeb 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gll0198 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9417
Polymers32,3081
Non-polymers2,6346
Water25214
1
A: Gll0198 protein
hetero molecules

A: Gll0198 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,88314
Polymers64,6152
Non-polymers5,26812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7480 Å2
ΔGint-42 kcal/mol
Surface area24200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.250, 129.250, 82.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
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
Components on special symmetry positions
IDModelComponents
11A-1414-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Gll0198 protein


Mass: 32307.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain ATCC 29082 / PCC 7421) (bacteria)
Strain: ATCC 29082 / PCC 7421 / Gene: gll0198 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NP59

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Non-polymers , 5 types, 20 molecules

#2: Chemical ChemComp-RET / RETINAL


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


Mass: 678.940 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#4: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#5: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 307 K / Method: vapor diffusion, hanging drop / pH: 3.4
Details: 2.6-2.8 M NaH2PO4, 1,6-hexanediol, triethylene glycol, zinc acetate, n-Octyl-beta-D-Glucoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→42.79 Å / Num. obs: 19500 / % possible obs: 96.37 % / Redundancy: 1.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.04428 / Rpim(I) all: 0.04428 / Rrim(I) all: 0.06262 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 0.2155 / Num. unique obs: 19313 / CC1/2: 0.891 / Rpim(I) all: 0.2155 / Rrim(I) all: 0.3047

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472)refinement
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DDL

3ddl


Resolution: 2→42.79 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2444 --
Rwork0.2303 --
obs-19313 96.37 %
Refinement stepCycle: LAST / Resolution: 2→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 144 14 2082
LS refinement shellResolution: 2→2.072 Å /
RfactorNum. reflection
Rfree0.2607 -
Rwork0.2605 1873

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