[English] 日本語
Yorodumi- PDB-7mo6: Guanosine Monophosphate Synthase from Aspergillus fumigatus Af293 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mo6 | ||||||
---|---|---|---|---|---|---|---|
Title | Guanosine Monophosphate Synthase from Aspergillus fumigatus Af293 | ||||||
Components | GMP synthase [glutamine-hydrolyzing] | ||||||
Keywords | LIGASE / Guanosine monophosphate synthase / purine biosynthesis | ||||||
Function / homology | Function and homology information GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / pyrophosphatase activity / glutamine metabolic process / ATP binding Similarity search - Function | ||||||
Biological species | Aspergillus fumigatus Af293 (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Nguyen, S. / Bruning, J.B. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Structural insights into the antifungal drug target guanosine monophosphate synthase from Aspergillus fumigatus. Authors: Nguyen, S. / Jovcevski, B. / Pukala, T.L. / Bruning, J.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7mo6.cif.gz | 409.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7mo6.ent.gz | 334.9 KB | Display | PDB format |
PDBx/mmJSON format | 7mo6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/7mo6 ftp://data.pdbj.org/pub/pdb/validation_reports/mo/7mo6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2ywcS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 59607.223 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A229XUE6, GMP synthase (glutamine-hydrolysing) #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.43 % |
---|---|
Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 21% PEG 3350, 0.05 M Bis-Tris pH 6.5 |
-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: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→44.94 Å / Num. obs: 47553 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.089 / Rrim(I) all: 0.227 / Net I/σ(I): 6.1 / Num. measured all: 311610 / Scaling rejects: 354 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2YWC Resolution: 2.3→39.94 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.23 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.94 Å2 / Biso mean: 59.3144 Å2 / Biso min: 29.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→39.94 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|