- PDB-3o83: Structure of BasE N-terminal domain from Acinetobacter baumannii ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3o83
Title
Structure of BasE N-terminal domain from Acinetobacter baumannii bound to 2-(4-n-dodecyl-1,2,3-triazol-1-yl)-5'-O-[N-(2-hydroxybenzoyl)sulfamoyl]adenosine
Components
Peptide arylation enzyme
Keywords
LIGASE / Adenylation of 2 / 3-dihydroxybenzoate and transfer to pantetheine cofactor of BasF / Non-Ribosomal Peptide Synthetase (NRPS)
Function / homology
Function and homology information
2,3-dihydroxybenzoate--[aryl-carrier protein] ligase / siderophore biosynthetic process Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O
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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 DIFFERENCES AS FOUND IN GENBANK ENTRY ZP_04661818.
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Experimental details
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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: 57.92 %
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
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 26, 2010
Radiation
Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Crystal Type Si Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Resolution: 1.9→38.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.78 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21661
5308
5 %
RANDOM
Rwork
0.19383
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all
0.19497
101409
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obs
0.19497
101409
94.43 %
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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: MASK
Displacement parameters
Biso mean: 26.45 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.62 Å2
-0 Å2
-0 Å2
2-
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0.03 Å2
0 Å2
3-
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-1.65 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→38.95 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6788
0
109
513
7410
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
7077
X-RAY DIFFRACTION
r_angle_refined_deg
1.236
1.974
9646
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.713
5
874
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.46
24.438
329
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.901
15
1123
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.679
15
39
X-RAY DIFFRACTION
r_chiral_restr
0.08
0.2
1074
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
5437
X-RAY DIFFRACTION
r_mcbond_it
0.622
1.5
4344
X-RAY DIFFRACTION
r_mcangle_it
1.179
2
7017
X-RAY DIFFRACTION
r_scbond_it
1.735
3
2733
X-RAY DIFFRACTION
r_scangle_it
3.007
4.5
2625
LS refinement shell
Resolution: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.306
244
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Rwork
0.294
4728
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obs
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60.36 %
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