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Yorodumi- PDB-8g8p: F420-2/GTP(GDP) complex of F420-gamma glutamyl ligase (CofE) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g8p | ||||||
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Title | F420-2/GTP(GDP) complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus | ||||||
Components | Coenzyme F420:L-glutamate ligase | ||||||
Keywords | LIGASE / ligase substrate complex | ||||||
Function / homology | Function and homology information coenzyme F420-0:L-glutamate ligase / coenzyme F420-1:gamma-L-glutamate ligase / coenzyme F420-0:L-glutamate ligase activity / coenzyme F420-1:gamma-L-glutamate ligase activity / F420-0 metabolic process / GTP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus DSM 4304 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Bashiri, G. / Squire, C.J. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2024 Title: Poly-gamma-glutamylation of biomolecules. Authors: Bashiri, G. / Bulloch, E.M.M. / Bramley, W.R. / Davidson, M. / Stuteley, S.M. / Young, P.G. / Harris, P.W.R. / Naqvi, M.S.H. / Middleditch, M.J. / Schmitz, M. / Chang, W.C. / Baker, E.N. / Squire, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8g8p.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g8p.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8g8p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8g8p_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8g8p_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8g8p_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 8g8p_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/8g8p ftp://data.pdbj.org/pub/pdb/validation_reports/g8/8g8p | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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 AAA
#1: Protein | Mass: 27423.568 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea) Gene: cofE, AF_2256 / Production host: Escherichia coli (E. coli) References: UniProt: O28028, coenzyme F420-0:L-glutamate ligase, coenzyme F420-1:gamma-L-glutamate ligase |
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-Non-polymers , 7 types, 134 molecules
#2: Chemical | ChemComp-F42 / | ||||||
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#3: Chemical | ChemComp-GTP / | ||||||
#4: Chemical | ChemComp-GDP / | ||||||
#5: Chemical | #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-SO4 / | #8: 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: 1.95 Å3/Da / Density % sol: 36.88 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.8 M ammonium sulfate, 0.1 M citrate pH 4.5, 2 mM GTP, 5 mM Mn2+, 1 mM F420-2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→48.3 Å / Num. obs: 19796 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rpim(I) all: 0.039 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.83→1.88 Å / Num. unique obs: 990 / CC1/2: 0.599 / Rpim(I) all: 0.333 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→48.298 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.397 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.172 / ESU R Free: 0.139 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.422 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→48.298 Å
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Refine LS restraints |
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LS refinement shell |
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