[English] 日本語
Yorodumi- PDB-5fnp: High resolution Zn containing Iron sulfur cluster repair protein YtfE -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fnp | ||||||
---|---|---|---|---|---|---|---|
Title | High resolution Zn containing Iron sulfur cluster repair protein YtfE | ||||||
Components | IRON-SULFUR CLUSTER REPAIR PROTEIN YTFE | ||||||
Keywords | OXIDOREDUCTASE / NITRIC OXIDE / IRON-SULFUR CLUSTER REPAIR / DI-FE CENTER. | ||||||
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: 1.8 Å | ||||||
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. ...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. | ||||||
Citation | Journal: Chemistry / Year: 2016 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fnp.cif.gz | 184.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fnp.ent.gz | 148.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fnp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/5fnp ftp://data.pdbj.org/pub/pdb/validation_reports/fn/5fnp | HTTPS FTP |
---|
-Related structure data
Related structure data | 5fnnSC 5fnyC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24851.516 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P69506, nitric oxide reductase (cytochrome c) #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | OXO GROUP (OXO): U-OXO BRIDGE IN THE METAL CLUSTER | Sequence details | OUR CONSTRUCT INCLUDED MUTATIONS ON C30 AND C31 TO A | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.25 % / Description: NONE |
---|---|
Crystal grow | pH: 8.5 / Details: 0.1 M TRIS/HCL PH 8.5 20% PEG8000 0.2 M MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 |
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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25.9 Å / Num. obs: 51147 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.11 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.42 / % possible all: 74 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FNN Resolution: 1.8→25.87 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.418 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 44.525 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|