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Open data
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Basic information
Entry | Database: PDB / ID: 7o1t | ||||||||||||
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Title | Fe(CO)2CNCl species bound [HydE from T. Maritima | ||||||||||||
![]() | [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 / organonitrogen compound biosynthetic process / : / 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 / organonitrogen compound biosynthetic process / : / 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 | ![]() | 179.6 KB | Display | ![]() |
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PDB format | ![]() | 137.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.6 MB | Display | ![]() |
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Full document | ![]() | 3.6 MB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 33.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o1oC ![]() 7o1pC ![]() 7o1sC ![]() 7o25C ![]() 7o26C ![]() 3ciwS S: Starting model for refinement C: citing same article ( |
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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 , 11 types, 497 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/5X8.gif)
![](data/chem/img/CPS.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IOD.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/5X8.gif)
![](data/chem/img/CPS.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IOD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CYS / | ||||||||||||||||||
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#3: Chemical | #4: Chemical | ChemComp-CMO / #5: Chemical | #6: Chemical | ChemComp-PYR / | #7: Chemical | ChemComp-5X8 / | #8: Chemical | ChemComp-CPS / | #9: Chemical | ChemComp-SF4 / | #10: Chemical | ChemComp-CL / | #11: Chemical | ChemComp-IOD / | #12: 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: 2.26 Å3/Da / Density % sol: 45.54 % |
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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: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→43 Å / Num. obs: 113796 / % possible obs: 99.3 % / Redundancy: 4.7 % / CC1/2: 0.997 / Net I/σ(I): 8.76 |
Reflection shell | Resolution: 1.5→1.54 Å / Num. unique obs: 11102 / CC1/2: 0.52 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CIW Resolution: 1.5→9.93 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.27 / Phase error: 21.68 / 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: 93.69 Å2 / Biso mean: 24.5153 Å2 / Biso min: 10.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→9.93 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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