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Yorodumi- PDB-7uld: GTP complex of F420-gamma glutamyl ligase (CofE) from Archaeoglob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uld | ||||||
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Title | GTP 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: 1.3 Å | ||||||
Authors | Bashiri, G. / Squire, C.J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: A Universal Mechanism for Poly-glutamylation Authors: Bashiri, G. / Bramley, W. / Bulloch, E. / Stutely, S. / Middleditch, M. / Young, P. / Naqvi, M. / Harris, P. / 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 | 7uld.cif.gz | 125.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7uld.ent.gz | 94.4 KB | Display | PDB format |
PDBx/mmJSON format | 7uld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7uld_validation.pdf.gz | 791.8 KB | Display | wwPDB validaton report |
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Full document | 7uld_full_validation.pdf.gz | 791.8 KB | Display | |
Data in XML | 7uld_validation.xml.gz | 13 KB | Display | |
Data in CIF | 7uld_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/7uld ftp://data.pdbj.org/pub/pdb/validation_reports/ul/7uld | HTTPS FTP |
-Related structure data
Related structure data | 7uleC 7ulfC 2phnS 6vw3 6vw5 S: Starting model for refinement C: citing same article (ref.) |
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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 A
#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 , 6 types, 210 molecules
#2: Chemical | ChemComp-CO3 / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-GTP / | #6: Chemical | #7: 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 Å3/Da / Density % sol: 38.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.8 M ammonium sulfate, 0.1 M citrate pH 4.5, 2 mM GTP, 5 mM Mn2+ |
-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: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 25, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→46.6 Å / Num. obs: 55332 / % possible obs: 100 % / Redundancy: 28 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 27.2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2692 / CC1/2: 0.517 / Rpim(I) all: 0.693 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2phn Resolution: 1.3→43.04 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.112 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.049 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.57 Å2 / Biso mean: 17.499 Å2 / Biso min: 8.58 Å2
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Refinement step | Cycle: final / Resolution: 1.3→43.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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