+Open data
-Basic information
Entry | Database: PDB / ID: 6nwd | ||||||
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Title | X-ray Crystallographic structure of Gloeobacter rhodopsin | ||||||
Components | Gll0198 protein | ||||||
Keywords | TRANSPORT PROTEIN / Proton pump / Photoreceptor | ||||||
Function / homology | Function and homology information light-activated monoatomic ion channel activity / : / phototransduction / photoreceptor activity / membrane => GO:0016020 / identical protein binding Similarity search - Function | ||||||
Biological species | Gloeobacter violaceus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ernst, O.P. / Morizumi, T. / Ou, W.L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nwd.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nwd.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 6nwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nwd_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6nwd_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6nwd_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 6nwd_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/6nwd ftp://data.pdbj.org/pub/pdb/validation_reports/nw/6nwd | HTTPS FTP |
-Related structure data
Related structure data | 3ddlS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: 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 / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-D10 / | #5: Chemical | ChemComp-D12 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.14 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DDL Resolution: 2→42.79 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2→42.79 Å
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LS refinement shell | Resolution: 2→2.072 Å /
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