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- PDB-6bz0: 1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehyd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bz0 | ||||||
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Title | 1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Acinetobacter baumannii in Complex with FAD. | ||||||
![]() | Dihydrolipoyl dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Dihydrolipoyl Dehydrogenase / FAD. | ||||||
Function / homology | ![]() dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / cell redox homeostasis / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: 1.83 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Acinetobacter baumannii in Complex with FAD. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 739.3 KB | Display | ![]() |
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PDB format | ![]() | 610 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 78.1 KB | Display | |
Data in CIF | ![]() | 112.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5u8uS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 51378.758 Da / Num. of mol.: 4 / Mutation: V355I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81 Gene: lpdA, F911_00968, HMPREF0010_02914 / Plasmid: pMCSG53 / Production host: ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 22.6 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (G10), 0.2M Magnesium chloride, 0.1M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2017 / Details: C(111) |
Radiation | Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→30 Å / Num. obs: 150403 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.047 / Rrim(I) all: 0.093 / Rsym value: 0.08 / Χ2: 1.006 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 4 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7400 / CC1/2: 0.696 / Rpim(I) all: 0.466 / Rrim(I) all: 0.928 / Rsym value: 0.803 / Χ2: 1.001 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5U8U Resolution: 1.83→29.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.262 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.139 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.82 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→29.63 Å
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Refine LS restraints |
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