[English] 日本語
Yorodumi- PDB-6y88: IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y88 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex with substrate inhibitor rCdRP | |||||||||
Components | (Indole-3-glycerol phosphate ...) x 2 | |||||||||
Keywords | LYASE / Tryptophan biosynthesis / carboxylyase / ba8-barrel / indole synthesis | |||||||||
Function / homology | Function and homology information indole-3-glycerol-phosphate synthase / indole-3-glycerol-phosphate synthase activity / phosphoribosylanthranilate isomerase activity / tryptophan biosynthetic process Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09983451737 Å | |||||||||
Authors | Soderholm, A. / Selmer, M. | |||||||||
Funding support | Sweden, 2items
| |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structure and kinetics of indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa : Decarboxylation is not essential for indole formation. Authors: Soderholm, A. / Newton, M.S. / Patrick, W.M. / Selmer, M. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6y88.cif.gz | 855.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6y88.ent.gz | 661.9 KB | Display | PDB format |
PDBx/mmJSON format | 6y88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y88_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6y88_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 6y88_validation.xml.gz | 84.8 KB | Display | |
Data in CIF | 6y88_validation.cif.gz | 120.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/6y88 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/6y88 | HTTPS FTP |
-Related structure data
Related structure data | 3tsmS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
4 |
| ||||||||||||
5 |
| ||||||||||||
6 |
| ||||||||||||
7 |
| ||||||||||||
8 |
| ||||||||||||
Unit cell |
|
-Components
-Indole-3-glycerol phosphate ... , 2 types, 8 molecules ABCDEFHG
#1: Protein | Mass: 31458.074 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: trpC, DT376_13060 / Production host: Escherichia coli (E. coli) References: UniProt: A0A367MAM9, UniProt: P20577*PLUS, indole-3-glycerol-phosphate synthase #2: Protein | | Mass: 29909.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: trpC, DT376_13060 / Production host: Escherichia coli (E. coli) References: UniProt: A0A367MAM9, UniProt: P20577*PLUS, indole-3-glycerol-phosphate synthase |
---|
-Non-polymers , 5 types, 1145 molecules
#3: Chemical | ChemComp-137 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CIT / | #6: Chemical | ChemComp-PO4 / | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 56.38 % |
---|---|
Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 3.4 Details: 0.07 M Citric acid, 0.03 M Bis-Tris propane pH 3.4 (Condition G12 from PEG/Ion screen from Hampton Research) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→50 Å / Num. obs: 321139 / % possible obs: 100 % / Redundancy: 7.03 % / Biso Wilson estimate: 30.2458918458 Å2 / CC1/2: 0.994 / Net I/σ(I): 7.61 |
Reflection shell | Resolution: 2.099→2.23 Å / Mean I/σ(I) obs: 1.73 / Num. unique obs: 51980 / CC1/2: 0.73 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TSM Resolution: 2.09983451737→48.0433596166 Å / SU ML: 0.23247016633 / Cross valid method: FREE R-VALUE / σ(F): 1.1861589204 / Phase error: 21.7744224305 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.8851359205 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09983451737→48.0433596166 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|