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- PDB-5fnn: Iron and Selenomethionine containing Iron sulfur cluster repair p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fnn | ||||||
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Title | Iron and Selenomethionine containing Iron sulfur cluster repair protein YtfE | ||||||
![]() | IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE | ||||||
![]() | OXIDOREDUCTASE / NITRIC OXIDE / IRON-SULFUR CLUSTER REPAIR / DI-FE CENTER. | ||||||
Function / homology | ![]() response to nitrosative stress / protein repair / response to oxidative stress / iron ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lo, F.-C. / Hsieh, C.-C. / Maestre-Reyna, M. / Chen, C.-Y. / Ko, T.-P. / Horng, Y.-C. / Lai, Y.-C. / Chiang, Y.-W. / Chou, C.-M. / Chiang, C.-H. ...Lo, F.-C. / Hsieh, C.-C. / Maestre-Reyna, M. / Chen, C.-Y. / Ko, T.-P. / Horng, Y.-C. / Lai, Y.-C. / Chiang, Y.-W. / Chou, C.-M. / Chiang, C.-H. / Huang, W.-N. / Liaw, W.-F. | ||||||
![]() | ![]() Title: Crystal Structure of the Repair of Iron Centers Protein Ytfe and its Interaction with No Authors: Lo, F.-C. / Hsieh, C.-C. / Maestre-Reyna, M. / Chen, C.-Y. / Ko, T.-P. / Horng, Y.-C. / Lai, Y.-C. / Chiang, Y.-W. / Chou, C.-M. / Chiang, C.-H. / Huang, W.-N. / Liaw, W.-F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.7 KB | Display | ![]() |
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PDB format | ![]() | 145.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.8 KB | Display | ![]() |
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Full document | ![]() | 442.1 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25367.357 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P69506, nitric oxide reductase (cytochrome c) |
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-Non-polymers , 5 types, 83 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/O.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/FE.gif)
![](data/chem/img/O.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | OXO GROUP (OXO): U-OXO BRIDGE IN THE DIIRON CLUSTER |
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Sequence details | OUR CONSTRUCT INCLUDED MUTATIONS ON C30 AND C31 TO A |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.23 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M TRISCL PH8.5, 21% PEG4000, 0.2 M MGCL2, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2014 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→27.9 Å / Num. obs: 34895 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.37 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.67 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NONE Resolution: 2.09→77.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.346 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.091 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→77.58 Å
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Refine LS restraints |
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