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Open data
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Basic information
Entry | Database: PDB / ID: 7bhc | |||||||||
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Title | Escherichia coli YtfE E125L | |||||||||
![]() | Iron-sulfur cluster repair protein YtfE | |||||||||
![]() | METAL BINDING PROTEIN / di-iron | |||||||||
Function / homology | ![]() response to nitrosative stress / protein repair / response to oxidative stress / iron ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Silva, L.S.O. / Matias, P.M. / Romao, C.V. / Saraiva, L.M. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 330.8 KB | Display | ![]() |
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PDB format | ![]() | 228.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.9 KB | Display | ![]() |
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Full document | ![]() | 441.7 KB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 30.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bhaC ![]() 7bhbC ![]() 5fnnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: (0.944226147871, -0.0172804015172, 0.328843989454), (-0.0145666260032, -0.999836493473, -0.0107144634333), (0.328975371545, 0.00532672912634, -0.944323477879)Vector: 15. ...NCS oper: (Code: given Matrix: (0.944226147871, -0.0172804015172, 0.328843989454), Vector: |
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Components
#1: Protein | Mass: 24704.359 Da / Num. of mol.: 2 / Mutation: C30A C31A E125L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: ytfE, b4209, JW4167 Production host: ![]() ![]() 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 59.43 % / Description: needle shaped |
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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, Sodium Chloride |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→53.2 Å / Num. obs: 41865 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.049 / Rrim(I) all: 0.096 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.87→1.98 Å / Rmerge(I) obs: 1.232 / Num. unique obs: 4140 / CC1/2: 0.36 / Rpim(I) all: 0.767 / % possible all: 99.74 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5FNN Resolution: 1.87→53.2 Å / SU ML: 0.2826 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7718 / 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: 48.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→53.2 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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