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- PDB-3o82: Structure of BasE N-terminal domain from Acinetobacter baumannii ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3o82 | ||||||
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Title | Structure of BasE N-terminal domain from Acinetobacter baumannii bound to 5'-O-[N-(2,3-dihydroxybenzoyl)sulfamoyl] adenosine | ||||||
![]() | Peptide arylation enzyme | ||||||
![]() | LIGASE / Adenylation of 2 / 3-dihydroxybenzoate and transfer to pantetheine cofactor of BasF / Non-Ribosomal Peptide Synthetase (NRPS) | ||||||
Function / homology | ![]() 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / siderophore biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Drake, E.J. / Duckworth, B.P. / Neres, J. / Aldrich, C.C. / Gulick, A.M. | ||||||
![]() | ![]() Title: Biochemical and structural characterization of bisubstrate inhibitors of BasE, the self-standing nonribosomal peptide synthetase adenylate-forming enzyme of acinetobactin synthesis. Authors: Drake, E.J. / Duckworth, B.P. / Neres, J. / Aldrich, C.C. / Gulick, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186 KB | Display | ![]() |
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PDB format | ![]() | 143.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 32.6 KB | Display | |
Data in CIF | ![]() | 44.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3o83C ![]() 3o84C ![]() 1mdbS C: citing same article ( 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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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 5 - 435 / Label seq-ID: 7 - 437
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Components
#1: Protein | Mass: 60868.270 Da / Num. of mol.: 2 / Fragment: BasE / Mutation: P45L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B2HVG8, UniProt: A0A7U3Y1M5*PLUS, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases #2: Chemical | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Sequence details | THIS ENTRY USES A UNIPROT REFERENCE THAT IS FOR A DIFFERENT STRAIN OF A. BAUMANNI. THESE CHANGES ...THIS ENTRY USES A UNIPROT REFERENCE THAT IS FOR A DIFFERENT STRAIN OF A. BAUMANNI. THESE CHANGES ARE STRAIN RELATED DIFFERENCE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.73 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 5-15% PEG 8000, 5% MPD, 250-600 mM CaCl2, 50 mM BTP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2008 |
Radiation | Monochromator: Side-scattering cuberoot I-beam bent single crystal; asymetric cut 12.2 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 39977 / Num. obs: 38979 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 56.6 Å2 / Rsym value: 0.131 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.377 / % possible all: 81.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MDB residues 1-430 Resolution: 2.7→40 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.896 / SU B: 10.586 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.475 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.064 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3323 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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