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Open data
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Basic information
Entry | Database: PDB / ID: 1mdf | ||||||
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Title | CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE | ||||||
![]() | 2,3-dihydroxybenzoate-AMP ligase | ||||||
![]() | LIGASE / adenylation domain / peptide synthetase / antibiotic biosynthesis / siderophore formation | ||||||
Function / homology | ![]() 2,3-dihydroxybenzoate-[aryl-carrier protein] ligase / 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / siderophore biosynthetic process / ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | May, J.J. / Kessler, N. / Marahiel, M.A. / Stubbs, M.T. | ||||||
![]() | ![]() Title: Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases. Authors: May, J.J. / Kessler, N. / Marahiel, M.A. / Stubbs, M.T. | ||||||
History |
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Remark 999 | SEQUENCE Author states the sequence has recently been deposited at NCBI with the acquisition number ...SEQUENCE Author states the sequence has recently been deposited at NCBI with the acquisition number bankit484943. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.3 KB | Display | ![]() |
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PDB format | ![]() | 89.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.8 KB | Display | ![]() |
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Full document | ![]() | 392.1 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1md9SC ![]() 1mdbC S: Starting model for refinement C: citing same article ( |
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Similar 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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Components
#1: Protein | Mass: 59988.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P40871, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.06 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8.6 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Detector | Date: Mar 10, 2001 |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 16523 / Observed criterion σ(I): 0 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 17099 / % possible obs: 96.5 % / Num. measured all: 42630 / Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS % possible obs: 92.4 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.68 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MD9 Resolution: 2.5→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.5→100 Å
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Refinement | *PLUS Rfactor Rfree: 0.275 / Rfactor Rwork: 0.204 / % reflection Rfree: 10 % | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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