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- PDB-7o25: Complex-B bound [FeFe]-hydrogenase maturase HydE from T. maritima... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7o25 | ||||||||||||
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Title | Complex-B bound [FeFe]-hydrogenase maturase HydE from T. maritima (reaction triggered in the crystal) | ||||||||||||
![]() | [FeFe] hydrogenase maturase subunit HydE | ||||||||||||
![]() | METAL BINDING PROTEIN / Radical SAM protein / Hydrogenase maturase / metalloprotein | ||||||||||||
Function / homology | ![]() water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / : / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity ...water-soluble vitamin biosynthetic process / : / sulfur compound biosynthetic process / : / Oxidoreductases; Acting on a sulfur group of donors / : / : / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / transferase activity / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Rohac, R. / Martin, L. / Liu, L. / Basu, D. / Tao, L. / Britt, R.D. / Rauchfuss, T. / Nicolet, Y. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Crystal Structure of the [FeFe]-Hydrogenase Maturase HydE Bound to Complex-B. Authors: Rohac, R. / Martin, L. / Liu, L. / Basu, D. / Tao, L. / Britt, R.D. / Rauchfuss, T.B. / Nicolet, Y. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.3 KB | Display | ![]() |
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PDB format | ![]() | 143.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.5 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o1oC ![]() 7o1pC ![]() 7o1sC ![]() 7o1tC ![]() 7o26C ![]() 3ciwS C: citing same article ( S: Starting model for refinement |
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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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | [ Mass: 41009.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q9X0Z6, Oxidoreductases; Acting on a sulfur group of donors |
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-Non-polymers , 16 types, 390 molecules ![](data/chem/img/CYS.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CPS.gif)
![](data/chem/img/5X8.gif)
![](data/chem/img/TAM.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/CYN.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CPS.gif)
![](data/chem/img/5X8.gif)
![](data/chem/img/TAM.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CYS / | ||||||||||||||||||||||||||
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#3: Chemical | ChemComp-FE2 / | ||||||||||||||||||||||||||
#4: Chemical | #5: Chemical | ChemComp-CYN / | #6: Chemical | ChemComp-PYR / | #7: Chemical | ChemComp-SAM / | #8: Chemical | ChemComp-MET / | #9: Chemical | ChemComp-GOL / | #10: Chemical | #11: Chemical | ChemComp-5X8 / | #12: Chemical | ChemComp-TAM / | #13: Chemical | ChemComp-EDO / | #14: Chemical | ChemComp-SF4 / | #15: Chemical | ChemComp-PO4 / #16: Chemical | ChemComp-CL / | #17: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.78 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG; LiSO4; Tris pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9805 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→47.15 Å / Num. obs: 159228 / % possible obs: 99.6 % / Redundancy: 14.4 % / CC1/2: 0.999 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.34→1.42 Å / Num. unique obs: 12982 / CC1/2: 0.729 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CIW Resolution: 1.34→47.15 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.55 / Stereochemistry target values: ML
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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: 109.09 Å2 / Biso mean: 23.3075 Å2 / Biso min: 9.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.34→47.15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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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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