+Open data
-Basic information
Entry | Database: PDB / ID: 7bha | ||||||
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Title | Escherichia coli YtfE | ||||||
Components | Iron-sulfur cluster repair protein YtfE | ||||||
Keywords | METAL BINDING PROTEIN / di-iron | ||||||
Function / homology | Function and homology information protein repair / response to nitrosative stress / 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: 2.19 Å | ||||||
Authors | Silva, L.S.O. / Matias, P.M. / Romao, C.V. / Saraiva, L.M. | ||||||
Funding support | Portugal, 1items
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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 | 7bha.cif.gz | 211.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bha.ent.gz | 139.3 KB | Display | PDB format |
PDBx/mmJSON format | 7bha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/7bha ftp://data.pdbj.org/pub/pdb/validation_reports/bh/7bha | HTTPS FTP |
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-Related structure data
Related structure data | 7bhbC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: givenMatrix: (0.937154934584, -0.0127426509258, 0.348680732808), (-0.0132090181169, -0.999912216244, -0.00104002253238), (0.348663376948, -0.00363106786838, -0.937240985511)Vector: - ...NCS oper: (Code: given Matrix: (0.937154934584, -0.0127426509258, 0.348680732808), Vector: |
-Components
#1: Protein | Mass: 24720.316 Da / Num. of mol.: 2 / Mutation: C30A C31A 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 | ChemComp-FE / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.19 Å3/Da / Density % sol: 54.5 % / Description: needle shapped |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / 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: ALBA / Beamline: XALOC / Wavelength: 1.7314 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7314 Å / Relative weight: 1 |
Reflection | Resolution: 2.188→59.05 Å / Num. obs: 23568 / % possible obs: 87 % / Redundancy: 6.4 % / Biso Wilson estimate: 37.78 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.062 / Rrim(I) all: 0.16 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.188→2.188 Å / Rmerge(I) obs: 1.548 / Num. unique obs: 549 / CC1/2: 0.354 / % possible all: 40.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FNN Resolution: 2.19→59.05 Å / SU ML: 0.2773 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3811 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: Structure refined with anomalous data
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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: 57.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→59.05 Å
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Refine LS restraints |
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LS refinement shell |
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