[English] 日本語
Yorodumi- PDB-1qcd: CRYSTAL STRUCTURES OF ADENINE PHOSPHORIBOSYLTRANSFERASE FROM LEIS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qcd | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURES OF ADENINE PHOSPHORIBOSYLTRANSFERASE FROM LEISHMANIA DONOVANI | ||||||
Components | ADENINE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / DINUCLEOTIDE BINDING FOLD | ||||||
Function / homology | Function and homology information adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / nucleotide binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.48 Å | ||||||
Authors | Phillips, C.L. / Ullman, B. / Brennan, R.G. / Hill, C.P. | ||||||
Citation | Journal: EMBO J. / Year: 1999 Title: Crystal structures of adenine phosphoribosyltransferase from Leishmania donovani. Authors: Phillips, C.L. / Ullman, B. / Brennan, R.G. / Hill, C.P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qcd.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qcd.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qcd_validation.pdf.gz | 425.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1qcd_full_validation.pdf.gz | 427.3 KB | Display | |
Data in XML | 1qcd_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 1qcd_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/1qcd ftp://data.pdbj.org/pub/pdb/validation_reports/qc/1qcd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26096.920 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q27679 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.88 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: AMMONIUM SULFATE, SODIUM CITRATE, MAGNESIUM CHLORIDE, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: OTHER / Detector: AREA DETECTOR / Date: Sep 1, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 40.7 Å2 |
Reflection | *PLUS Highest resolution: 2.48 Å / Lowest resolution: 18.6 Å / Num. obs: 9680 / % possible obs: 87.2 % / Num. measured all: 33527 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 50.1 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 4.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.48→18.57 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.48→18.57 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.48→2.64 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|