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Yorodumi- PDB-8fi3: Bifunctional ligase/repressor BirA from Klebsiella pneumoniae com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fi3 | |||||||||
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Title | Bifunctional ligase/repressor BirA from Klebsiella pneumoniae complexed with biotin (Domain Swapped Dimer) | |||||||||
Components | Bifunctional ligase/repressor BirA | |||||||||
Keywords | TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | |||||||||
Function / homology | Function and homology information biotin-[biotin carboxyl-carrier protein] ligase / biotin-[acetyl-CoA-carboxylase] ligase activity / protein modification process / regulation of DNA-templated transcription / DNA binding / ATP binding Similarity search - Function | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Bifunctional ligase/repressor BirA from Klebsiella pneumoniae complexed with biotin (Domain Swapped Dimer) Authors: Liu, L. / Battaile, K.P. / Lovell, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fi3.cif.gz | 248.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fi3.ent.gz | 199.9 KB | Display | PDB format |
PDBx/mmJSON format | 8fi3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/8fi3 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/8fi3 | HTTPS FTP |
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-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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Unit cell |
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-Components
#1: Protein | Mass: 36502.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: birA / Plasmid: Klpnc.17896.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0W7ZMT5 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.57 Å3/Da / Density % sol: 52.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus H2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM ...Details: Morpheus H2: 20%(v/v) Ethylene glycol, 10%(w/v) PEG 8000, 100 mM Imidazole/MES, pH 6.5, 20 mM DL-Glutamic acid, 20 mM DL-Alanine; 20 mM Glycine, 20 mM DL-Lysine monohydrochloride and 20 mM DL-Serine 20mg/ml protein and 4 mM Biotin, KlpnC.17896.a.B1.PW39036 at 30 mg/mL. Tray: Liu-S-043 drop C5, Puck: PSL0113, Cryo: 150% Morpheus G3. |
-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: 0.9786 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 10, 2022 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→47.82 Å / Num. obs: 17266 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.062 / Rrim(I) all: 0.162 / Χ2: 1 / Net I/σ(I): 9.7 / Num. measured all: 114603 |
Reflection shell | Resolution: 2.9→3.08 Å / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 1.158 / Num. measured all: 17046 / Num. unique obs: 2720 / CC1/2: 0.555 / Rpim(I) all: 0.502 / Rrim(I) all: 1.265 / Χ2: 0.99 / Net I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.82 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.66 / 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: 2.9→47.82 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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