[English] 日本語
Yorodumi- PDB-1pgo: CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pgo | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTALLOGRAPHIC STUDY OF COENZYME, COENZYME ANALOGUE AND SUBSTRATE BINDING IN 6-PHOSPHOGLUCONATE DEHYDROGENASE: IMPLICATIONS FOR NADP SPECIFICITY AND THE ENZYME MECHANISM | ||||||
Components | 6-PHOSPHOGLUCONATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE (CHOH(D)-NADP+(A)) | ||||||
Function / homology | Function and homology information phosphogluconate 2-dehydrogenase activity / D-gluconate catabolic process / phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) / phosphogluconate dehydrogenase (decarboxylating) activity / pentose-phosphate shunt, oxidative branch / pentose-phosphate shunt / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Adams, M.J. / Phillips, C. / Gover, S. | ||||||
Citation | Journal: Structure / Year: 1994 Title: Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism. Authors: Adams, M.J. / Ellis, G.H. / Gover, S. / Naylor, C.E. / Phillips, C. #1: Journal: To be Published Title: The Structure of 6-Phosphogluconate Dehydrogenase Refined at 2 Angstroms Resolution Authors: Phillips, C. / Gover, S. / Adams, M.J. #2: Journal: Acta Crystallogr.,Sect.B / Year: 1991 Title: The Structure of 6-Phosphogluconate Dehydrogenase Refined at 2.5 Angstroms Resolution Authors: Adams, M.J. / Gover, S. / Leaback, R. / Phillips, C. / Somers, D.O'N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pgo.cif.gz | 113.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pgo.ent.gz | 87.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pgo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pgo_validation.pdf.gz | 693.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1pgo_full_validation.pdf.gz | 702.7 KB | Display | |
Data in XML | 1pgo_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 1pgo_validation.cif.gz | 36.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/1pgo ftp://data.pdbj.org/pub/pdb/validation_reports/pg/1pgo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: CIS PROLINE - PRO 67 |
-Components
#1: Protein | Mass: 52905.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ovis aries (sheep) References: UniProt: P00349, phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-NDP / | #4: Water | ChemComp-HOH / | Nonpolymer details | THE NDP GROUP (NADPH) CARRIES A ---- CHARGE. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.87 % |
---|---|
Crystal grow | *PLUS Method: other / Details: Somers, D.O., (1991) Protein Expr. Purif., 2, 385. |
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 17995 / % possible obs: 92.2 % / Num. measured all: 46279 / Rmerge(I) obs: 0.067 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Rfactor Rwork: 0.17 / Rfactor obs: 0.17 / Highest resolution: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor obs: 0.17 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|