+Open data
-Basic information
Entry | Database: PDB / ID: 5eru | ||||||
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Title | Ternary complex of GephE - ADP - Molybdenum cluster | ||||||
Components | Gephyrin | ||||||
Keywords | TRANSFERASE / Molybdenum cluster / Moco / Wco / Moco biosynthesis / ternary complex | ||||||
Function / homology | Function and homology information Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization / gamma-aminobutyric acid receptor clustering ...Molybdenum cofactor biosynthesis / molybdopterin cofactor biosynthetic process / glycine receptor clustering / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / establishment of synaptic specificity at neuromuscular junction / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / postsynaptic specialization / gamma-aminobutyric acid receptor clustering / nitrate reductase activity / inhibitory synapse / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / response to metal ion / postsynaptic specialization membrane / molybdopterin cofactor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic specialization, intracellular component / GABA-ergic synapse / protein targeting / synapse assembly / tubulin binding / synaptic membrane / establishment of protein localization / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / postsynapse / postsynaptic membrane / molecular adaptor activity / postsynaptic density / cytoskeleton / signaling receptor binding / neuronal cell body / dendrite / ATP binding / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kasaragod, V.B. / Schindelin, H. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Structure / Year: 2016 Title: Structural Framework for Metal Incorporation during Molybdenum Cofactor Biosynthesis. Authors: Kasaragod, V.B. / Schindelin, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eru.cif.gz | 272.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eru.ent.gz | 222.4 KB | Display | PDB format |
PDBx/mmJSON format | 5eru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eru_validation.pdf.gz | 867.8 KB | Display | wwPDB validaton report |
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Full document | 5eru_full_validation.pdf.gz | 868.3 KB | Display | |
Data in XML | 5eru_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 5eru_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/5eru ftp://data.pdbj.org/pub/pdb/validation_reports/er/5eru | HTTPS FTP |
-Related structure data
Related structure data | 5erqC 5errC 5ersC 5ertC 5ervC 4pd0S S: Starting model for refinement C: citing same article (ref.) |
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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: 45652.395 Da / Num. of mol.: 1 / Fragment: UNP residues 318-736 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gphn, Gph / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03555 |
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-Non-polymers , 9 types, 454 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-ADP / | #6: Chemical | ChemComp-PO4 / | #7: Chemical | ChemComp-MO / #8: Chemical | ChemComp-MOO / | #9: Chemical | ChemComp-MG / | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate, 0.02 M calcium chloride, 24% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.6187 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6187 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→74.52 Å / Num. obs: 65106 / % possible obs: 100 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 20.8 % / Rmerge(I) obs: 1.724 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PD0 Resolution: 1.6→43.84 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→43.84 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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