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- PDB-8sbz: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8sbz | |||||||||
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Title | Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (NAD bound, No sulfate hexagonal form) | |||||||||
![]() | 2,3-dihydroxybenzoate-2,3-dehydrogenase | |||||||||
![]() | OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | |||||||||
Function / homology | ![]() 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase / 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase activity / siderophore biosynthetic process / nucleotide binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (NAD bound, No sulfate hexagonal form) Authors: Liu, L. / Lovell, S. / Battaile, K.P. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.3 KB | Display | ![]() |
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PDB format | ![]() | 157.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fwmS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 27572.984 Da / Num. of mol.: 2 / Mutation: A2N, A3G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: EAE_13665 / Plasmid: KlaeA.01365.a.B1 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: Berkeley F3: 20% PEG 5000 MME, 0.2 M Ammonium Acetate. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. 2mM NAD added to the protein prior to crystallization. Plate: plate 13163, well F3, drop 2, ...Details: Berkeley F3: 20% PEG 5000 MME, 0.2 M Ammonium Acetate. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. 2mM NAD added to the protein prior to crystallization. Plate: plate 13163, well F3, drop 2, Puck: PSL-0616, Cryo: 20% PEG 200 + 80% crystallant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 14, 2022 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→109.25 Å / Num. obs: 38930 / % possible obs: 100 % / Redundancy: 39.5 % / CC1/2: 1 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.017 / Rrim(I) all: 0.104 / Χ2: 0.99 / Net I/σ(I): 23.4 / Num. measured all: 1537256 |
Reflection shell | Resolution: 1.9→1.95 Å / % possible obs: 99.9 % / Redundancy: 37.4 % / Rmerge(I) obs: 2.364 / Num. measured all: 104905 / Num. unique obs: 2806 / CC1/2: 0.92 / Rpim(I) all: 0.389 / Rrim(I) all: 2.396 / Χ2: 0.97 / Net I/σ(I) obs: 1.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FWM Resolution: 1.9→75.33 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.36 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→75.33 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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