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- PDB-1upx: The crystal structure of the Hybrid Cluster Protein from Desulfov... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1upx | ||||||
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Title | The crystal structure of the Hybrid Cluster Protein from Desulfovibrio desulfuricans containing molecules in the oxidized and reduced states. | ||||||
![]() | HYDROXYLAMINE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / HYBRID CLUSTER / REDUCED IRON-SULFUR / OXIDIZED IRON-SULFUR | ||||||
Function / homology | ![]() hydroxylamine reductase / hydroxylamine reductase activity / response to hydrogen peroxide / peroxidase activity / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Aragao, D. / Macedo, S. / Mitchell, E.P. / Lindley, P.F. | ||||||
![]() | ![]() Title: Structure of the Hybrid Cluster Protein (Hcp) from Desulfovibrio Desulfuricans Atcc 27774 Containing Molecules in the Oxidized and Reduced States Authors: Macedo, S. / Aragao, D. / Mitchell, E.P. / Lindley, P.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.6 KB | Display | ![]() |
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PDB format | ![]() | 203.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 895.8 KB | Display | ![]() |
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Full document | ![]() | 904.5 KB | Display | |
Data in XML | ![]() | 56.5 KB | Display | |
Data in CIF | ![]() | 89.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e2uS 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9807, -0.1955, -0.0081), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 58595.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: CUBANE CLUSTER [4FE-4S], HYBRID CLUSTER [4FE-3S], [4FE-3S-3O] Source: (natural) ![]() |
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-Non-polymers , 5 types, 1684 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/SF3.gif)
![](data/chem/img/FSO.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF3.gif)
![](data/chem/img/FSO.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MES / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | FUNCTION: CATALYZES REDUCTION OF HYDROXYLAM |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 25% PEG 8000, 0.1M MES PH6.0, TEMPERATURE 279 KELVIN, pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 279 K / pH: 7.6 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 1, 2000 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→30 Å / Num. obs: 280898 / % possible obs: 84.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 6.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 1.15→1.19 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 1.3 / % possible all: 70 |
Reflection | *PLUS Highest resolution: 1.15 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 70 % / Redundancy: 1.3 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 1.3 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E2U Resolution: 1.25→27.52 Å / SU B: 0.606 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.042 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 8.521 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→27.52 Å
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Refinement | *PLUS Rfactor Rfree: 0.153 / Rfactor Rwork: 0.14 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.25 Å / Lowest resolution: 1.29 Å / Rfactor Rfree: 0.221 / Num. reflection Rfree: 125 / Rfactor Rwork: 0.206 / Num. reflection Rwork: 13493 |