+Open data
-Basic information
Entry | Database: PDB / ID: 1mdf | ||||||
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Title | CRYSTAL STRUCTURE OF DhbE IN ABSENCE OF SUBSTRATE | ||||||
Components | 2,3-dihydroxybenzoate-AMP ligase | ||||||
Keywords | LIGASE / adenylation domain / peptide synthetase / antibiotic biosynthesis / siderophore formation | ||||||
Function / homology | Function and homology information 2,3-dihydroxybenzoate-[aryl-carrier protein] ligase / (2,3-dihydroxybenzoyl)adenylate synthase activity / siderophore biosynthetic process / ligase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | May, J.J. / Kessler, N. / Marahiel, M.A. / Stubbs, M.T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mdf.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mdf.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mdf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/1mdf ftp://data.pdbj.org/pub/pdb/validation_reports/md/1mdf | HTTPS FTP |
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-Related structure data
Related structure data | 1md9SC 1mdbC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Bacillus subtilis (bacteria) / Strain: ATCC 21332 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 pREP4 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: X-RAY DIFFRACTION |
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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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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