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Open data
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Basic information
Entry | Database: PDB / ID: 1bou | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF LIGAB | ||||||
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![]() | DIOXYGENASE / EXTRADIOL TYPE DIOXYGENASE / OXIDOREDUCTASE | ||||||
Function / homology | ![]() protocatechuate 4,5-dioxygenase / protocatechuate 4,5-dioxygenase activity / : / ferrous iron binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sugimoto, K. / Senda, T. / Fukuda, M. / Mitsui, Y. | ||||||
![]() | ![]() Title: Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions. Authors: Sugimoto, K. / Senda, T. / Aoshima, H. / Masai, E. / Fukuda, M. / Mitsui, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.8 KB | Display | ![]() |
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PDB format | ![]() | 140.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 392.1 KB | Display | ![]() |
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Full document | ![]() | 408.6 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.481, -0.853, -0.203), Vector: |
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Components
#1: Protein | Mass: 15567.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22635, protocatechuate 4,5-dioxygenase #2: Protein | Mass: 33322.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22636, protocatechuate 4,5-dioxygenase #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.4 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: pH 7.4 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Sugimoto, K., (1999) Protein Peptide Lett., 6, 55. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Mar 9, 1998 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→60 Å / Num. obs: 43335 / % possible obs: 86.5 % / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 2.9 / % possible all: 58 |
Reflection | *PLUS Num. measured all: 80490 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.2→60 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 43259 / Rfactor obs: 0.16 / Rfactor Rfree: 0.216 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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