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Yorodumi- PDB-6e6q: 1.20 A resolution structure of the C-terminally truncated [2Fe-2S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e6q | |||||||||
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Title | 1.20 A resolution structure of the C-terminally truncated [2Fe-2S] ferredoxin (Bfd) from Pseudomonas aeruginosa | |||||||||
Components | Bacterioferritin-associated ferredoxin | |||||||||
Keywords | ELECTRON TRANSPORT / IRON MOBILIZATION / [2Fe-2S] ferredoxin / Bfd / anion binding site | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | |||||||||
Authors | Lovell, S. / Wijerathne, H. / Battaile, K.P. / Yao, H. / Wang, Y. / Rivera, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2018 Title: Bfd, a New Class of [2Fe-2S] Protein That Functions in Bacterial Iron Homeostasis, Requires a Structural Anion Binding Site. Authors: Wijerathne, H. / Yao, H. / Wang, Y. / Lovell, S. / Battaile, K.P. / Rivera, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e6q.cif.gz | 61.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e6q.ent.gz | 44.1 KB | Display | PDB format |
PDBx/mmJSON format | 6e6q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e6q_validation.pdf.gz | 426.3 KB | Display | wwPDB validaton report |
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Full document | 6e6q_full_validation.pdf.gz | 426.4 KB | Display | |
Data in XML | 6e6q_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 6e6q_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/6e6q ftp://data.pdbj.org/pub/pdb/validation_reports/e6/6e6q | HTTPS FTP |
-Related structure data
Related structure data | 6e6rC 6e6sC 4e6kS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 6169.035 Da / Num. of mol.: 2 / Fragment: M1-L56 / Mutation: C43S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: bfd, AO896_12000, AO964_01120, AOY09_04877, C8257_08100, CAZ03_03910, CAZ10_19915, CGU42_05470, CSB93_2785, PAERUG_E15_London_28_01_14_09195, PAMH19_1562, RW109_RW109_02290 Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Variant (production host): ARCTIC EXPRESS RIL / References: UniProt: A0A069Q647, UniProt: Q9HY80*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 1.91 Å3/Da / Density % sol: 35.63 % / Mosaicity: 0.24 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30% (v/v) 2-methyl-2,4-pentanediol, 100 mM sodium acetate, 20 mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.2→39.61 Å / Num. obs: 28905 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 11.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.3 / Num. measured all: 96242 | |||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4E6K Resolution: 1.2→39.61 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 15.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 48.53 Å2 / Biso mean: 15.6781 Å2 / Biso min: 8.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→39.61 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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