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Yorodumi- PDB-8sqr: Crystal Structure of Bacterioferritin (Bfr) from Brucella abortus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8sqr | |||||||||
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Title | Crystal Structure of Bacterioferritin (Bfr) from Brucella abortus (iron bound, 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: 1.65 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 (iron bound, 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 | 8sqr.cif.gz | 89.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8sqr.ent.gz | 65.2 KB | Display | PDB format |
PDBx/mmJSON format | 8sqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8sqr_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 8sqr_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 8sqr_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 8sqr_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sq/8sqr ftp://data.pdbj.org/pub/pdb/validation_reports/sq/8sqr | 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 8 types, 137 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-FE2 / #6: Chemical | ChemComp-ACT / | #7: Chemical | ChemComp-HEM / | #8: Chemical | ChemComp-MPD / ( | #9: Water | ChemComp-HOH / | |
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-Details
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: 3.19 Å3/Da / Density % sol: 61.46 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 21% MPD, 0.4M MgCl2, 0.1M Ac pH 4.6, BrabA.00028.a.A1.PW39164 at 10 mg/mL. Plate: Liu-S-066, well G9, 2. Puck: PSL-1801, Cryo: 35% MPD + crystallant. 5 minute soak in 25 mM ferrous ammonium sulfate in cryo 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: 1.65→46.15 Å / Num. obs: 30324 / % possible obs: 100 % / Redundancy: 58.1 % / CC1/2: 1 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.022 / Rrim(I) all: 0.168 / Χ2: 1 / Net I/σ(I): 22.8 / Num. measured all: 1761720 |
Reflection shell | Resolution: 1.65→1.68 Å / % possible obs: 100 % / Redundancy: 60.9 % / Rmerge(I) obs: 3.939 / Num. measured all: 95600 / Num. unique obs: 1571 / CC1/2: 0.728 / Rpim(I) all: 0.507 / Rrim(I) all: 3.972 / Χ2: 0.98 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→32.63 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 20.17 / 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: 1.65→32.63 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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