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Yorodumi- PDB-4hs5: Frataxin from Psychromonas ingrahamii as a model to study stabili... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hs5 | ||||||
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Title | Frataxin from Psychromonas ingrahamii as a model to study stability modulation within CyaY protein family | ||||||
Components | Protein CyaY | ||||||
Keywords | METAL BINDING PROTEIN / pFXN / frataxin / CyaY / Psychromonas ingrahamii / Frataxin-like domain / CyaY protein family (pfam ID PF01491) / Iron homeostasis-redox balance | ||||||
Function / homology | Function and homology information iron chaperone activity / iron-sulfur cluster assembly / ferroxidase activity / ferric iron binding / ferrous iron binding / 2 iron, 2 sulfur cluster binding / intracellular iron ion homeostasis / cytosol Similarity search - Function | ||||||
Biological species | Psychromonas ingrahamii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Roman, E.A. / Cousido-siah, A. / Mitschler, A. / Podjarny, A. / Santos, J. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Frataxin from Psychromonas ingrahamii as a model to study stability modulation within the CyaY protein family Authors: Roman, E.A. / Faraj, S.E. / Cousido-Siah, A. / Mitschler, A. / Podjarny, A. / Santos, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hs5.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hs5.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 4hs5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hs5_validation.pdf.gz | 429 KB | Display | wwPDB validaton report |
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Full document | 4hs5_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 4hs5_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4hs5_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/4hs5 ftp://data.pdbj.org/pub/pdb/validation_reports/hs/4hs5 | HTTPS FTP |
-Related structure data
Related structure data | 1ew4S S: Starting model for refinement |
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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: 12295.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Kanamycin resistance, IPTG inducible / Source: (gene. exp.) Psychromonas ingrahamii (bacteria) / Strain: 37 / Gene: cyaY, Ping_0042 / Plasmid: pJexpress411:56977 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: A1SR01 #2: Water | ChemComp-HOH / | |
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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: 1.86 Å3/Da / Density % sol: 33.78 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 20mM sodium acetate, 200mM MgCl2, 29.5% PEG 4000, pH 4.80, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 177 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9191 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 2, 2012 |
Radiation | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9191 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 31292 / Num. obs: 31292 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.45→1.5 Å / % possible all: 97.1 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1EW4 Resolution: 1.45→31.186 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8479 / SU ML: 0.17 / σ(F): 0 / Phase error: 22.53 / Stereochemistry target values: Engh & Huber
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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 max: 58.38 Å2 / Biso mean: 15.7965 Å2 / Biso min: 2.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→31.186 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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