[English] 日本語
Yorodumi- PDB-1fp3: CRYSTAL STRUCTURE OF N-ACYL-D-GLUCOSAMINE 2-EPIMERASE FROM PORCIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fp3 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF N-ACYL-D-GLUCOSAMINE 2-EPIMERASE FROM PORCINE KIDNEY | ||||||
Components | N-ACYL-D-GLUCOSAMINE 2-EPIMERASE | ||||||
Keywords | ISOMERASE / ALPHA/ALPHA-BARREL / N-acyl-D-glucosamine 2-epimerase | ||||||
Function / homology | Function and homology information N-acylglucosamine 2-epimerase / N-acylglucosamine 2-epimerase activity / N-acetylmannosamine metabolic process / N-acetylglucosamine metabolic process / peptidase inhibitor activity / N-acetylneuraminate catabolic process Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Itoh, T. / Mikami, B. / Maru, I. / Ohta, Y. / Hashimoto, W. / Murata, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of N-acyl-D-glucosamine 2-epimerase from porcine kidney at 2.0 A resolution. Authors: Itoh, T. / Mikami, B. / Maru, I. / Ohta, Y. / Hashimoto, W. / Murata, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fp3.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fp3.ent.gz | 134.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/1fp3 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/1fp3 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer related by the two-fold axis. |
-Components
#1: Protein | Mass: 46465.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Tissue: KIDNEY / Plasmid: PEP114 / Production host: Escherichia coli (E. coli) / References: UniProt: P17560, N-acylglucosamine 2-epimerase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.16 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 6000, sodium citrate, ammonium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: Maru, I., (1996) J. Biochem., 120, 481. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Apr 19, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→25 Å / Num. all: 49059 / Num. obs: 39143 / % possible obs: 82.1 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.92→1.98 Å / Redundancy: 2.54 % / Rmerge(I) obs: 0.056 / Num. unique all: 1270 / % possible all: 82.1 |
Reflection | *PLUS Num. measured all: 124509 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→14.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 667176.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.37 Å2 / ksol: 0.342 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→14.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.294 / % reflection Rfree: 10 % / Rfactor Rwork: 0.249 |