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Yorodumi- PDB-3u16: Structure of BasE N-terminal domain from Acinetobacter baumannii ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u16 | ||||||
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Title | Structure of BasE N-terminal domain from Acinetobacter baumannii bound to 6-(p-benzyloxy)phenyl-1-(pyridin-4-ylmethyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid. | ||||||
Components | Peptide arylation enzyme | ||||||
Keywords | LIGASE / ANL Superfamily / adenylating enzyme / 2 / 3-dihydroxybenzoate:Aryl Carrier protein ligase / BasF | ||||||
Function / homology | Function and homology information 2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / siderophore biosynthetic process Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Gulick, A.M. / Drake, E.J. / Aldrich, C.C. / Neres, J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Non-nucleoside inhibitors of BasE, an adenylating enzyme in the siderophore biosynthetic pathway of the opportunistic pathogen Acinetobacter baumannii. Authors: Neres, J. / Engelhart, C.A. / Drake, E.J. / Wilson, D.J. / Fu, P. / Boshoff, H.I. / Barry 3rd, C.E. / Gulick, A.M. / Aldrich, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u16.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u16.ent.gz | 154.2 KB | Display | PDB format |
PDBx/mmJSON format | 3u16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u16_validation.pdf.gz | 982.1 KB | Display | wwPDB validaton report |
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Full document | 3u16_full_validation.pdf.gz | 992.3 KB | Display | |
Data in XML | 3u16_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 3u16_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/3u16 ftp://data.pdbj.org/pub/pdb/validation_reports/u1/3u16 | HTTPS FTP |
-Related structure data
Related structure data | 3u17C 3o84S 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60868.270 Da / Num. of mol.: 2 / Mutation: P45L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB900 / Gene: ACICU_02578, basE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B2HVG8, UniProt: A0A7U3Y1M5*PLUS, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases |
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-Non-polymers , 5 types, 521 molecules
#2: Chemical | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MPD / ( | #5: Chemical | ChemComp-MRD / ( | #6: Water | ChemComp-HOH / | |
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-Details
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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.9 % |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 24, 2010 |
Radiation | Monochromator: SSRL 11-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 84673 / Num. obs: 82980 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.542 / % possible all: 88.4 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3O84 Resolution: 2.1→39.65 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.47 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→39.65 Å
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Refine LS restraints |
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LS refinement shell |
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