[English] 日本語
Yorodumi- PDB-1ovm: Crystal structure of Indolepyruvate decarboxylase from Enterobact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ovm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Indolepyruvate decarboxylase from Enterobacter cloacae | ||||||
Components | Indole-3-pyruvate decarboxylase | ||||||
Keywords | LYASE / thiamine diphosphate / indole-3-acetic acid / indolepyruvate / tdp dependent enzyme / decarboxylase | ||||||
Function / homology | Function and homology information auxin biosynthetic process / indolepyruvate decarboxylase / indolepyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Schutz, A. / Sandalova, T. / Ricagno, S. / Hubner, G. / Konig, S. / Schneider, G. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2003 Title: Crystal structure of thiamindiphosphate-dependent indolepyruvate decarboxylase from Enterobacter cloacae, an enzyme involved in the biosynthesis of the plant hormone indole-3-acetic acid Authors: Schutz, A. / Sandalova, T. / Ricagno, S. / Hubner, G. / Konig, S. / Schneider, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ovm.cif.gz | 413.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ovm.ent.gz | 337.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ovm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ovm_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ovm_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1ovm_validation.xml.gz | 85.2 KB | Display | |
Data in CIF | 1ovm_validation.cif.gz | 113.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ov/1ovm ftp://data.pdbj.org/pub/pdb/validation_reports/ov/1ovm | HTTPS FTP |
-Related structure data
Related structure data | 1zpdS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 60087.289 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: IPDC / Plasmid: pIP362 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P23234, indolepyruvate decarboxylase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-TPP / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.71 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEGmme, Na citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→29.56 Å / Num. all: 63376 / Num. obs: 63376 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44.9 Å2 / Limit h max: 49 / Limit h min: 0 / Limit k max: 57 / Limit k min: 0 / Limit l max: 40 / Limit l min: 0 / Observed criterion F max: 2754137.27 / Observed criterion F min: 25.6 / Rsym value: 0.087 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.65→2.77 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.369 / % possible all: 99.9 |
Reflection | *PLUS Num. obs: 63426 / Num. measured all: 315465 / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.369 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZPD Resolution: 2.65→29.56 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||
Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 22.125 Å2 / ksol: 0.33713 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso max: 93.33 Å2 / Biso mean: 33.42 Å2 / Biso min: 2.47 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→29.56 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.65→2.77 Å / Rfactor Rfree error: 0.014
| |||||||||||||||||||||||||
Xplor file |
| |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|