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Open data
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Basic information
Entry | Database: PDB / ID: 3vyt | ||||||
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Title | Crystal structure of the HypC-HypD-HypE complex (form I inward) | ||||||
![]() | (Hydrogenase expression/formation protein ...) x 3 | ||||||
![]() | METAL BINDING PROTEIN/TRANSFERASE / [NiFe] hydrogenase maturation / METAL BINDING PROTEIN-TRANSFERASE complex | ||||||
Function / homology | ![]() carbon dioxide binding / carbon monoxide binding / protein maturation / 4 iron, 4 sulfur cluster binding / iron ion binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Watanabe, S. / Miki, K. | ||||||
![]() | ![]() Title: Crystal structures of the HypCD complex and the HypCDE ternary complex: transient intermediate complexes during [NiFe] hydrogenase maturation Authors: Watanabe, S. / Matsumi, R. / Atomi, H. / Imanaka, T. / Miki, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.8 KB | Display | ![]() |
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PDB format | ![]() | 125.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.5 KB | Display | ![]() |
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Full document | ![]() | 486.6 KB | Display | |
Data in XML | ![]() | 30.8 KB | Display | |
Data in CIF | ![]() | 42.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vyrC ![]() 3vysC ![]() 3vyuC ![]() 2z1cS ![]() 2z1dS ![]() 2z1eS 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
-Hydrogenase expression/formation protein ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 8133.478 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 41925.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 35954.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 160 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SF4 / | ||||
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#5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 50mM MES, 12-16% PEG400, 10mM magnesium chloride, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 34520 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 50.7 Å2 / Rsym value: 0.039 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 2.25→2.3 Å / Redundancy: 2 % / Mean I/σ(I) obs: 22.3 / % possible all: 80.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2Z1C, 2Z1D, 2Z1E Resolution: 2.25→34.79 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3484493.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.2869 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→34.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.39 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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