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Yorodumi- PDB-8sbw: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sbw | |||||||||
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Title | Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (Apo, orthorhombic form) | |||||||||
Components | 2,3-dihydroxybenzoate-2,3-dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | |||||||||
Function / homology | Function and homology information 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 | Klebsiella aerogenes KCTC 2190 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal Structure of 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase from Klebsiella aerogenes (Apo, orthorhombic form) Authors: Liu, L. / Lovell, S. / Battaile, K.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8sbw.cif.gz | 178 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sbw.ent.gz | 139.9 KB | Display | PDB format |
PDBx/mmJSON format | 8sbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sbw_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
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Full document | 8sbw_full_validation.pdf.gz | 464.8 KB | Display | |
Data in XML | 8sbw_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 8sbw_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sb/8sbw ftp://data.pdbj.org/pub/pdb/validation_reports/sb/8sbw | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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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.) Klebsiella aerogenes KCTC 2190 (bacteria) Gene: EAE_13665 / Plasmid: KlaeA.01365.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3FXS4 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 1.96 Å3/Da / Density % sol: 37.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.4 Details: 0.6 M ammonium sulfate, 0.1M sodium acetate pH 4.4. KlaeA.01365.a.B1.PW39175 at 21.8 mg/mL. Plate: liu-S-078 well A7, Puck: PSL-0604, Cryo: 2.5 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å |
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: 1.75→67.26 Å / Num. obs: 44457 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Χ2: 1.03 / Net I/σ(I): 17.8 / Num. measured all: 590368 |
Reflection shell | Resolution: 1.75→1.8 Å / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 1.994 / Num. measured all: 43754 / Num. unique obs: 3234 / CC1/2: 0.773 / Rpim(I) all: 0.559 / Rrim(I) all: 2.072 / Χ2: 1.08 / Net I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→42.88 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.78 / 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: 1.75→42.88 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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