+Open data
-Basic information
Entry | Database: PDB / ID: 7bhb | |||||||||
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Title | Escherichia coli YtfE E159L | |||||||||
Components | Iron-sulfur cluster repair protein YtfE | |||||||||
Keywords | METAL BINDING PROTEIN / di-iron | |||||||||
Function / homology | Function and homology information response to nitrosative stress / protein repair / response to oxidative stress / iron ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | |||||||||
Authors | Silva, L.S.O. / Matias, P.M. / Romao, C.V. / Saraiva, M.L. | |||||||||
Funding support | Portugal, 2items
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Citation | Journal: Front Microbiol / Year: 2021 Title: Structural Basis of RICs Iron Donation for Iron-Sulfur Cluster Biogenesis. Authors: Silva, L.S.O. / Matias, P.M. / Romao, C.V. / Saraiva, L.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bhb.cif.gz | 310.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bhb.ent.gz | 212.2 KB | Display | PDB format |
PDBx/mmJSON format | 7bhb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bhb_validation.pdf.gz | 444.7 KB | Display | wwPDB validaton report |
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Full document | 7bhb_full_validation.pdf.gz | 451.2 KB | Display | |
Data in XML | 7bhb_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 7bhb_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/7bhb ftp://data.pdbj.org/pub/pdb/validation_reports/bh/7bhb | HTTPS FTP |
-Related structure data
Related structure data | 7bhaC 7bhcC 5fnnS 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: 24704.361 Da / Num. of mol.: 2 / Mutation: C30A C31A E159L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: ytfE, b4209, JW4167 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P69506 #2: Chemical | #3: 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: 2.48 Å3/Da / Density % sol: 50.45 % / Description: needle shapped |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris-HCl, PEG 4000, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Mar 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→86.81 Å / Num. obs: 11106 / % possible obs: 55.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 47.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.052 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.36→2.64 Å / Rmerge(I) obs: 0.828 / Num. unique obs: 556 / CC1/2: 0.568 / Rpim(I) all: 0.479 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FNN Resolution: 2.36→46.4 Å / SU ML: 0.3637 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 43.004 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.36→46.4 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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