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- PDB-2d0w: Crystal structure of cytochrome cL from Hyphomicrobium denitrificans -
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Open data
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Basic information
Entry | Database: PDB / ID: 2d0w | ||||||
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Title | Crystal structure of cytochrome cL from Hyphomicrobium denitrificans | ||||||
![]() | cytochrome cL | ||||||
![]() | ELECTRON TRANSPORT / electron transfer / cytochrome | ||||||
Function / homology | ![]() methanol metabolic process / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nojiri, M. / Hira, D. / Yamaguchi, K. / Suzuki, S. | ||||||
![]() | ![]() Title: Crystal structures of cytochrome c(L) and methanol dehydrogenase from Hyphomicrobium denitrificans: structural and mechanistic insights into interactions between the two proteins Authors: Nojiri, M. / Hira, D. / Yamaguchi, K. / Okajima, T. / Tanizawa, K. / Suzuki, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.8 KB | Display | ![]() |
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PDB format | ![]() | 70.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 22.3 KB | Display | |
Data in CIF | ![]() | 32 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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Components
#1: Protein | Mass: 18583.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: PEG10000, zinc sulfate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 22, 2004 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→29.24 Å / Num. all: 23538 / Num. obs: 22502 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 12 Å2 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.3956 Å2 / ksol: 0.348205 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.98→29.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.11 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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