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- PDB-2wlb: Adrenodoxin-like ferredoxin Etp1fd(516-618) of Schizosaccharomyce... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wlb | ||||||
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Title | Adrenodoxin-like ferredoxin Etp1fd(516-618) of Schizosaccharomyces pombe mitochondria | ||||||
![]() | ELECTRON TRANSFER PROTEIN 1, MITOCHONDRIAL | ||||||
![]() | ELECTRON TRANSPORT / IRON-SULFUR / MITOCHONDRIA / IRON / TRANSPORT / FERREDOXIN / ADRENODOXIN-LIKE / METAL-BINDING | ||||||
Function / homology | ![]() Heme biosynthesis / : / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / heme A biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors / [2Fe-2S] cluster assembly / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding ...Heme biosynthesis / : / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / heme A biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors / [2Fe-2S] cluster assembly / oxidoreductase activity, acting on NAD(P)H / iron-sulfur cluster binding / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mueller, J.J. / Hannemann, F. / Schiffler, B. / Bernhardt, R. / Heinemann, U. | ||||||
![]() | ![]() Title: Structural and Thermodynamic Characterization of the Adrenodoxin-Like Domain of the Electron-Transfer Protein Etp1 from Schizosaccharomyces Pombe. Authors: Mueller, J.J. / Hannemann, F. / Schiffler, B. / Ewen, K.M. / Kappl, R. / Heinemann, U. / Bernhardt, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.7 KB | Display | ![]() |
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PDB format | ![]() | 37.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.8 KB | Display | ![]() |
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Full document | ![]() | 450.3 KB | Display | |
Data in XML | ![]() | 9.2 KB | Display | |
Data in CIF | ![]() | 11.7 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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Components
#1: Protein | Mass: 11306.626 Da / Num. of mol.: 2 / Fragment: ADRENODOXIN-LIKE DOMAIN, RESIDUES 516-618 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.6 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: VAPOUR DIFFUSION, SITTING DROP, 4 DEGR. CENTIGRADE. RESERVOIR: 0.04M HEPES,1.8M NA-CITRATE, 3% GLYCEROL,PH7.0. PROTEIN SOLUTION: 18.4MG/ML PROTEIN, 20MM POTASSIUMPHOSPHATE,PH7.4. 0.3 PLUS 0.3 MICROLITER DROPLET. |
-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 6, 2004 |
Radiation | Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 8006 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 56.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.6→2.78 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.4 / % possible all: 92.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1E6E,1AYF,1L6V,2BT6 Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.626 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.463 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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