[English] 日本語
Yorodumi- PDB-7ulf: l-glutamate/GTP complex of F420-gamma glutamyl ligase (CofE) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ulf | ||||||
---|---|---|---|---|---|---|---|
Title | l-glutamate/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: 1.61 Å | ||||||
Authors | Bashiri, G. / Squire, C.J. | ||||||
Funding support | 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ulf.cif.gz | 68 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ulf.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 7ulf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ulf_validation.pdf.gz | 756.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7ulf_full_validation.pdf.gz | 756.6 KB | Display | |
Data in XML | 7ulf_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 7ulf_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/7ulf ftp://data.pdbj.org/pub/pdb/validation_reports/ul/7ulf | HTTPS FTP |
-Related structure data
Related structure data | 7uldC 7uleC 2phnS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#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 | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-GGL / | ||||
#3: Chemical | ChemComp-GTP / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.17 % |
---|---|
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+, 1 mM L-glutamate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 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: 1.61→43.04 Å / Num. obs: 29419 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rpim(I) all: 0.035 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.61→1.64 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1435 / CC1/2: 0.544 / Rpim(I) all: 0.645 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2phn Resolution: 1.61→43.04 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.394 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.093 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.31 Å2 / Biso mean: 25.412 Å2 / Biso min: 15.25 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.61→43.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.61→1.652 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|