+Open data
-Basic information
Entry | Database: PDB / ID: 1md9 | ||||||
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Title | CRYSTAL STRUCTURE OF DhbE IN COMPLEX WITH DHB AND AMP | ||||||
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-dihydroxybenzoate--[aryl-carrier protein] ligase / siderophore biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.8 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 | 1md9.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1md9.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 1md9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1md9_validation.pdf.gz | 456.2 KB | Display | wwPDB validaton report |
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Full document | 1md9_full_validation.pdf.gz | 480.9 KB | Display | |
Data in XML | 1md9_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 1md9_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/1md9 ftp://data.pdbj.org/pub/pdb/validation_reports/md/1md9 | HTTPS FTP |
-Related 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: 60363.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: M15 ATCC 21332 / Production host: Escherichia coli (E. coli) References: UniProt: P40871, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Chemical | ChemComp-AMP / |
#3: Chemical | ChemComp-DBH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.92 % | |||||||||||||||||||||||||||||||||||
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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 23, 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: 2.8→100 Å / Num. obs: 13234 / Observed criterion σ(I): 0 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 14081 / % possible obs: 95 % / Num. measured all: 38167 / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 90.9 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 12.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.8→100 Å
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Refinement | *PLUS Highest resolution: 2.8 Å / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.232 / % reflection Rfree: 10 % | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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