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- PDB-1ovm: Crystal structure of Indolepyruvate decarboxylase from Enterobact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ovm | ||||||
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Title | Crystal structure of Indolepyruvate decarboxylase from Enterobacter cloacae | ||||||
![]() | Indole-3-pyruvate decarboxylase | ||||||
![]() | LYASE / thiamine diphosphate / indole-3-acetic acid / indolepyruvate / tdp dependent enzyme / decarboxylase | ||||||
Function / homology | ![]() auxin biosynthetic process / indolepyruvate decarboxylase / indolepyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schutz, A. / Sandalova, T. / Ricagno, S. / Hubner, G. / Konig, S. / Schneider, G. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 413.7 KB | Display | ![]() |
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PDB format | ![]() | 337.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1zpdS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 60087.289 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-TPP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.71 % | ||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→29.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.77 Å / Rfactor Rfree error: 0.014
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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