[English] 日本語
Yorodumi- PDB-8d5g: Crystal structure of dihydropteroate synthase (folP-SMZ_B27) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d5g | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of dihydropteroate synthase (folP-SMZ_B27) from soil uncultured bacterium in complex with 6-hydroxymethyl-7,8-dihydropterin pyrophosphate | ||||||
Components | folP-SMZ_B27 | ||||||
Keywords | TRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / DIHYDROPTEROATE SYNTHASE | ||||||
Function / homology | 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE Function and homology information | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.78 Å | ||||||
Authors | Stogios, P.J. / Skarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of dihydropteroate synthase (folP-SMZ_B27) from soil uncultured bacterium in complex with 6-hydroxymethyl-7,8-dihydropterin pyrophosphate Authors: Stogios, P.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8d5g.cif.gz | 249.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8d5g.ent.gz | 178.1 KB | Display | PDB format |
PDBx/mmJSON format | 8d5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8d5g_validation.pdf.gz | 1009.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8d5g_full_validation.pdf.gz | 1016.3 KB | Display | |
Data in XML | 8d5g_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 8d5g_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/8d5g ftp://data.pdbj.org/pub/pdb/validation_reports/d5/8d5g | HTTPS FTP |
-Related structure data
Related structure data | 5visS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 29511.553 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: folP-SMZ_B27 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold #2: Chemical | #3: Chemical | ChemComp-CL / #4: 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: 2.61 Å3/Da / Density % sol: 52.91 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 25% (w/v) PEG 5K MME, 0.2 M ammonium sulfate, 0.1M sodium citrate dehydrate pH5.6, 1.2mM 6-hydroxymethyl-7,8-dihydropterin pyrophosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.78→25 Å / Num. obs: 16612 / % possible obs: 99.9 % / Redundancy: 16.2 % / Biso Wilson estimate: 48.25 Å2 / Rmerge(I) obs: 0.372 / Rpim(I) all: 0.093 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.78→2.83 Å / Redundancy: 9.5 % / Rmerge(I) obs: 1.245 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 808 / CC1/2: 0.576 / Rpim(I) all: 0.425 / % possible all: 99.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VIS Resolution: 2.78→24.82 Å / SU ML: 0.2729 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2422 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.39 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.78→24.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|