[English] 日本語
Yorodumi- PDB-1pox: THE REFINED STRUCTURES OF A STABILIZED MUTANT AND OF WILD-TYPE PY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pox | ||||||
---|---|---|---|---|---|---|---|
Title | THE REFINED STRUCTURES OF A STABILIZED MUTANT AND OF WILD-TYPE PYRUVATE OXIDASE FROM LACTOBACILLUS PLANTARUM | ||||||
Components | PYRUVATE OXIDASE | ||||||
Keywords | OXIDOREDUCTASE(OXYGEN AS ACCEPTOR) | ||||||
Function / homology | Function and homology information pyruvate oxidase / pyruvate oxidase activity / thiamine pyrophosphate binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Lactobacillus plantarum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Muller, Y.A. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: The refined structures of a stabilized mutant and of wild-type pyruvate oxidase from Lactobacillus plantarum. Authors: Muller, Y.A. / Schumacher, G. / Rudolph, R. / Schulz, G.E. #1: Journal: Science / Year: 1993 Title: Structure of the Thiamine-and Flavin-Dependent Enzyme Pyruvate Oxidase Authors: Muller, Y.A. / Schulz, G.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pox.cif.gz | 257.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pox.ent.gz | 203 KB | Display | PDB format |
PDBx/mmJSON format | 1pox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/1pox ftp://data.pdbj.org/pub/pdb/validation_reports/po/1pox | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Atom site foot note | 1: THE NA+ ION IS LOCATED ON A CRYSTALLOGRAPHIC TWO-FOLD AXIS. 2: HOH 801 - 806 ARE LOCATED ON A CRYSTALLOGRAPHIC TWO-FOLD AXIS. | |||||||||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.999948, 0.008221, -0.006109), Vector: Details | THE TETRAMER CAN BE GENERATED FROM THE ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSFORMATION: 1 0 0 0 0 -1 0 155.36 0 0 -1 0 THE TWO SUBUNITS OF THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT ARE RELATED BY A LOCAL TWOFOLD AXIS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 64207.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus plantarum (bacteria) / References: UniProt: P37063, pyruvate oxidase |
---|
-Non-polymers , 6 types, 749 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.96 % | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.2 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 88000 / % possible obs: 95.6 % / Num. measured all: 280000 / Rmerge(I) obs: 0.122 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.1→10 Å /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 10 Å / Num. reflection obs: 87755 / Rfactor obs: 0.162 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.7 |