[English] 日本語
Yorodumi- PDB-4j7u: Crystal structure of human sepiapterin reductase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j7u | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human sepiapterin reductase in complex with sulfathiazole | ||||||
Components | Sepiapterin reductase | ||||||
Keywords | OXIDOREDUCTASE/ANTIBIOTIC / Reductase / OXIDOREDUCTASE-ANTIBIOTIC complex | ||||||
Function / homology | Function and homology information sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming) / sepiapterin reductase (NADP+) activity / aldo-keto reductase (NADPH) activity / tetrahydrobiopterin biosynthetic process / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / NADP binding / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Groenlund Pedersen, M. / Pojer, F. / Johnsson, K. | ||||||
Citation | Journal: Science / Year: 2013 Title: Tetrahydrobiopterin biosynthesis as an off-target of sulfa drugs. Authors: Haruki, H. / Pedersen, M.G. / Gorska, K.I. / Pojer, F. / Johnsson, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4j7u.cif.gz | 213.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4j7u.ent.gz | 171.3 KB | Display | PDB format |
PDBx/mmJSON format | 4j7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j7u_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4j7u_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 4j7u_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 4j7u_validation.cif.gz | 53.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/4j7u ftp://data.pdbj.org/pub/pdb/validation_reports/j7/4j7u | HTTPS FTP |
-Related structure data
Related structure data | 4hwkSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 5 - 250 / Label seq-ID: 35 - 280
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 31290.029 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE References: UniProt: P35270, sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming) |
---|
-Non-polymers , 6 types, 169 molecules
#2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-YTZ / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.52 Å3/Da / Density % sol: 72.79 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.70 M ammonium sulphate, 0.1 M HEPES, 2 % w/v PEG 1000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2011 |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 162423 / Num. obs: 161097 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.45→2.59 Å / % possible all: 95.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HWK Resolution: 2.44→48.37 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.061 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.908 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.44→48.37 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1848 / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.443→2.507 Å / Total num. of bins used: 20
|