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Yorodumi- PDB-8sqp: Crystal Structure of Bacterioferritin (Bfr) from Brucella abortus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sqp | |||||||||
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Title | Crystal Structure of Bacterioferritin (Bfr) from Brucella abortus (Apo, F16L mutant) | |||||||||
Components | Bacterioferritin | |||||||||
Keywords | METAL BINDING PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | |||||||||
Function / homology | Function and homology information ferroxidase / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / heme binding / cytosol Similarity search - Function | |||||||||
Biological species | Brucella abortus 2308 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 Bacterioferritin (Bfr) from Brucella abortus (Apo, F16L mutant) Authors: Lovell, S. / Liu, L. / 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 | 8sqp.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sqp.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 8sqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sqp_validation.pdf.gz | 775.6 KB | Display | wwPDB validaton report |
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Full document | 8sqp_full_validation.pdf.gz | 775.8 KB | Display | |
Data in XML | 8sqp_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 8sqp_validation.cif.gz | 10.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/8sqp ftp://data.pdbj.org/pub/pdb/validation_reports/sq/8sqp | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18856.180 Da / Num. of mol.: 1 / Mutation: F16L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella abortus 2308 (bacteria) / Gene: bfr, BAB2_0675 / Plasmid: BrabA.00028.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2YKI4, ferroxidase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-HEM / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: Berkeley screen condition H3: 20% (w/v) PEG 3350, 100 mM Calcium chloride. BrabA.00028.a.A1.PW39164 at 10 mg/mL. Plate: 13090, well C3 drop 2. Puck: PSL-1806, Cryo: 30% PEG 3350 + crystallant PH range: ' |
-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: Mar 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: 2.05→45.75 Å / Num. obs: 15708 / % possible obs: 100 % / Redundancy: 39.2 % / CC1/2: 1 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.016 / Rrim(I) all: 0.102 / Χ2: 1 / Net I/σ(I): 28.2 / Num. measured all: 615703 |
Reflection shell | Resolution: 2.05→2.11 Å / % possible obs: 100 % / Redundancy: 41.8 % / Rmerge(I) obs: 3.359 / Num. measured all: 49707 / Num. unique obs: 1190 / CC1/2: 0.661 / Rpim(I) all: 0.523 / Rrim(I) all: 3.4 / Χ2: 0.97 / Net I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→31.08 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 24.27 / 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: 2.05→31.08 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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